element <mechanism> (global)
Namespace:
http://www.xml-cml.org/schema/cml2/react
Type:
anonymous complexType
Content:
complex, 4 attributes, 4 elements
Defined:
globally in cmlreact.xsd; see XML source
Includes:
definitions of 4 elements
Used:
at 1 location
XML Representation Summary
<mechanism
   
convention
 = 
 xsd:string
dictRef
 = 
 xsd:string
id
 = 
 xsd:string
title
 = 
 xsd:string
    >
   
Content: 
 name*, label*, description*, mechanismComponent*
</mechanism>
Content model elements (4):
description, label, mechanismComponent, name
Included in content model of elements (1):
reaction
Known Usage Locations
Annotation
<h:div class="summary">The mechanism of a reaction.</h:div> <h:div class="description"> <h:p>In some cases this may be a simple textual description or reference within a controlled vocabulary. In others it may describe the complete progress of the reaction, including topological or cartesian movement of atoms, bonds and electrons and annotation with varying quantities (e.g. energies). </h:p> <h:p> For named reaction mechanisms ("Diels-Alder", "ping-pong", "Claisen rearrangement", etc.) the <h:tt>name</h:tt> element should be used. For classification (e.g. "hydrolysis"), the <h:tt>label</h:tt> may be more appropriate. </h:p> <h:p>In more detailed cases the mechanism refers to components of the <h:tt>reaction</h:tt> element. Thus bond23 might be cleaved while bond19 is transformed (mapped) to bond99. The <h:tt>mechanismComponent</h:tt> can be used to refer to components and add annotation. This is still experimental.</h:p> </h:div> <h:div class="description"> <h:p>IUPAC Compendium of Chemical Terminology 2nd Edition (1997) describes a mechanism as: <h:blockquote>A detailed description of the process leading from the reactants to the products of a reaction, including a characterization as complete as possible of the composition, structure, energy and other properties of reaction intermediates, products and transition states. An acceptable mechanism of a specified reaction (and there may be a number of such alternative mechanisms not excluded by the evidence) must be consistent with the reaction stoichiometry, the rate law and with all other available experimental data, such as the stereochemical course of the reaction. Inferences concerning the electronic motions which dynamically interconvert successive species along the reaction path (as represented by curved arrows, for example) are often included in the description of a mechanism. It should be noted that for many reactions all this information is not available and the suggested mechanism is based on incomplete experimental data. It is not appropriate to use the term mechanism to describe a statement of the probable sequence in a set of stepwise reactions. That should be referred to as a reaction sequence, and not a mechanism.</h:blockquote> </h:p> <h:p>CMLReact provides reactionScheme and annotions to describe the reaction sequence and both it and <h:tt>mechanism</h:tt> could co-occur within a reactionScheme container.</h:p> </h:div> <h:div class="example" href="mechanism1.xml"/>
XML Source (see within schema source)
<xsd:element id="el.mechanism" name="mechanism">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">The mechanism of a reaction.</h:div>
<h:div class="description">
<h:p>
In some cases this may be a simple textual description or reference within a controlled vocabulary. In others it may describe the complete progress of the reaction, including topological or cartesian movement of atoms, bonds and electrons and annotation with varying quantities (e.g. energies).
</h:p>
<h:p>
For named reaction mechanisms ("Diels-Alder", "ping-pong", "Claisen rearrangement", etc.) the
<h:tt>name</h:tt>
element should be used. For classification (e.g. "hydrolysis"), the
<h:tt>label</h:tt>
may be more appropriate.
</h:p>
<h:p>
In more detailed cases the mechanism refers to components of the
<h:tt>reaction</h:tt>
element. Thus bond23 might be cleaved while bond19 is transformed (mapped) to bond99. The
<h:tt>mechanismComponent</h:tt>
can be used to refer to components and add annotation. This is still experimental.
</h:p>
</h:div>
<h:div class="description">
<h:p>
IUPAC Compendium of Chemical Terminology 2nd Edition (1997) describes a mechanism as:
<h:blockquote>
A detailed description of the process leading from the reactants to the
products of a reaction, including a characterization as complete as possible
of the composition, structure, energy and other properties of reaction
intermediates, products and transition states. An acceptable mechanism of
a specified reaction (and there may be a number of such alternative mechanisms
not excluded by the evidence) must be consistent with the reaction
stoichiometry, the rate law and with all other available experimental data,
such as the stereochemical course of the reaction. Inferences concerning
the electronic motions which dynamically interconvert successive species
along the reaction path (as represented by curved arrows, for example) are
often included in the description of a mechanism.
It should be noted that for many reactions all this information is not
available and the suggested mechanism is based on incomplete experimental
data. It is not appropriate to use the term mechanism to describe a
statement of the probable sequence in a set of stepwise reactions. That
should be referred to as a reaction sequence, and not a mechanism.
</h:blockquote>
</h:p>
<h:p>
CMLReact provides reactionScheme and annotions to describe the reaction sequence and both it and
<h:tt>mechanism</h:tt>
could co-occur within a reactionScheme container.
</h:p>
</h:div>
<h:div class="example" href="mechanism1.xml"/>
</xsd:documentation>
</xsd:annotation>
<xsd:complexType>
<xsd:sequence>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="name"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="label"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="description"/>
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="mechanismComponent"/>
</xsd:sequence>
<xsd:attributeGroup ref="title"/>
<xsd:attributeGroup ref="id"/>
<xsd:attributeGroup ref="convention"/>
<xsd:attributeGroup ref="dictRef"/>
</xsd:complexType>
</xsd:element>
Attribute Detail (all declarations; 4/4)
convention
Type:
namespaceRefType
Use:
optional
Defined:
locally within convention attributeGroup
<h:div class="summary">A reference to a convention.</h:div> <h:div class="description">There is no controlled vocabulary for conventions, but the author must ensure that the semantics are openly available and that there are mechanisms for implementation. The convention is inherited by all the subelements, so that a convention for <h:tt>molecule</h:tt> would by default extend to its <h:tt>bond</h:tt> and <h:tt>atom</h:tt> children. This can be overwritten if necessary by an explicit <h:tt>convention</h:tt>. <h:p>It may be useful to create conventions with namespaces (e.g. <h:tt>iupac:name</h:tt>). Use of <h:tt>convention</h:tt> will normally require non-STMML semantics, and should be used with caution. We would expect that conventions prefixed with "ISO" would be useful, such as ISO8601 for dateTimes.</h:p> <h:p>There is no default, but the conventions of STMML or the related language (e.g. CML) will be assumed.</h:p> </h:div> <h:div class="example" href="convGroup1.xml" id="ex"/>
XML Source (see within schema source)
<xsd:attribute id="att.convention" name="convention" type="namespaceRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to a convention.</h:div>
<h:div class="description">
There is no controlled vocabulary for conventions, but the author must ensure that the semantics are openly available and that there are mechanisms for implementation. The convention is inherited by all the subelements,
so that a convention for
<h:tt>molecule</h:tt>
would by default extend to its
<h:tt>bond</h:tt>
and
<h:tt>atom</h:tt>
children. This can be overwritten
if necessary by an explicit
<h:tt>convention</h:tt>
.
<h:p>
It may be useful to create conventions with namespaces (e.g.
<h:tt>iupac:name</h:tt>
).
Use of
<h:tt>convention</h:tt>
will normally require non-STMML semantics, and should be used with
caution. We would expect that conventions prefixed with "ISO" would be useful,
such as ISO8601 for dateTimes.
</h:p>
<h:p>
There is no default, but the conventions of STMML or the related language (e.g. CML) will be assumed.
</h:p>
</h:div>
<h:div class="example" href="convGroup1.xml" id="ex"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
dictRef
Type:
namespaceRefType
Use:
optional
Defined:
locally within dictRef attributeGroup
<h:div class="summary">A reference to a dictionary entry.</h:div> <h:div class="description">Elements in data instances such as _scalar_ may have a <h:tt>dictRef</h:tt> attribute to point to an entry in a dictionary. To avoid excessive use of (mutable) filenames and URIs we recommend a namespace prefix, mapped to a namespace URI in the normal manner. In this case, of course, the namespace URI must point to a real XML document containing _entry_ elements and validated against STMML Schema. <h:p>Where there is concern about the dictionary becoming separated from the document the dictionary entries can be physically included as part of the data instance and the normal XPointer addressing mechanism can be used.</h:p> <h:p>This attribute can also be used on _dictionary_ elements to define the namespace prefix</h:p> </h:div> <h:div class="example" href="dictRefGroup1.xml"/>
XML Source (see within schema source)
<xsd:attribute id="att.dictRef" name="dictRef" type="namespaceRefType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A reference to a dictionary entry.</h:div>
<h:div class="description">
Elements in data instances such as _scalar_ may have a
<h:tt>dictRef</h:tt>
attribute to point to an entry in a dictionary. To avoid excessive use of (mutable) filenames and URIs we recommend a namespace prefix, mapped to a namespace URI in the normal manner. In this case, of course, the namespace URI must point to a real XML document containing _entry_ elements and validated against STMML Schema.
<h:p>
Where there is concern about the dictionary becoming separated from the document the dictionary entries can be physically included as part of the data instance and the normal XPointer addressing mechanism can be used.
</h:p>
<h:p>
This attribute can also be used on _dictionary_ elements to define the namespace prefix
</h:p>
</h:div>
<h:div class="example" href="dictRefGroup1.xml"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
id
Type:
idType
Use:
optional
Defined:
locally within id attributeGroup
<h:div class="summary">An attribute providing a unique ID for an element.</h:div> <h:div class="description"/>
XML Source (see within schema source)
<xsd:attribute id="att.id" name="id" type="idType">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">
An attribute providing a unique ID for an element.
</h:div>
<h:div class="description"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
title
Type:
xsd:string, predefined
Use:
optional
Defined:
locally within title attributeGroup
<h:div class="summary">A title on an element.</h:div> <h:div class="description">No controlled value.</h:div> <h:div class="example" href="title1.xml"/>
XML Source (see within schema source)
<xsd:attribute id="att.title" name="title" type="xsd:string">
<xsd:annotation>
<xsd:documentation>
<h:div class="summary">A title on an element.</h:div>
<h:div class="description">No controlled value.</h:div>
<h:div class="example" href="title1.xml"/>
</xsd:documentation>
</xsd:annotation>
</xsd:attribute>
Content Element Detail (all declarations; 4/4)
description
Type:
anonymous complexType, mixed content
Defined:
by reference within (this) mechanism element
XML Source (see within schema source)
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="description"/>
label
Type:
anonymous complexType, complex content
Defined:
by reference within (this) mechanism element
XML Source (see within schema source)
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="label"/>
mechanismComponent
Type:
anonymous complexType, complex content
Defined:
by reference within (this) mechanism element
XML Source (see within schema source)
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="mechanismComponent"/>
name
Type:
anonymous complexType (extension of xsd:string), simple content
Defined:
by reference within (this) mechanism element
XML Source (see within schema source)
<xsd:element maxOccurs="unbounded" minOccurs="0" ref="name"/>
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