Docs for schema item mechanism in Chemical Markup Language (CML)

The mechanism of a reaction. 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). For named reaction mechanisms ("Diels-Alder", "ping-pong", "Claisen rearrangement", etc.) the name element should be used. For classification (e.g. "hydrolysis"), the label may be more appropriate. In more detailed cases the mechanism refers to components of the reaction element. Thus bond23 might be cleaved while bond19 is transformed (mapped) to bond99. The mechanismComponent can be used to refer to components and add annotation. This is still experimental. IUPAC Compendium of Chemical Terminology 2nd Edition (1997) describes a mechanism as: 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. CMLReact provides reactionScheme and annotions to describe the reaction sequence and both it and mechanism could co-occur within a reactionScheme container. 2006-02-28 PMR: changed content model to choice.

<xsd:element name="mechanism" id="el.mechanism"> <xsd:annotation> <xsd:documentation> <h:div class="summary" xmlns:h="http://www.w3.org/1999/xhtml">The mechanism of a reaction.</h:div> <h:div class="description" xmlns:h="http://www.w3.org/1999/xhtml"> <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" xmlns:h="http://www.w3.org/1999/xhtml"> <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="curation" xmlns:h="http://www.w3.org/1999/xhtml">2006-02-28 PMR: changed content model to choice.</h:div> <h:div class="example" href="mechanism1.xml" xmlns:h="http://www.w3.org/1999/xhtml" /> </xsd:documentation> </xsd:annotation> <xsd:complexType> <xsd:choice minOccurs="0" maxOccurs="unbounded"> <xsd:element ref="name" /> <xsd:element ref="label" /> <xsd:element ref="description" /> <xsd:element ref="mechanismComponent" /> </xsd:choice> <xsd:attributeGroup ref="title" /> <xsd:attributeGroup ref="id" /> <xsd:attributeGroup ref="convention" /> <xsd:attributeGroup ref="dictRef" /> </xsd:complexType> </xsd:element>

Definition Type:	Element
Name:	mechanism
Namespace:	http://www.xml-cml.org/schema
Containing Schema:	schema.xsd
Abstract
Documentation:	The mechanism of a reaction. 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). For named reaction mechanisms ("Diels-Alder", "ping-pong", "Claisen rearrangement", etc.) the name element should be used. For classification (e.g. "hydrolysis"), the label may be more appropriate. In more detailed cases the mechanism refers to components of the reaction element. Thus bond23 might be cleaved while bond19 is transformed (mapped) to bond99. The mechanismComponent can be used to refer to components and add annotation. This is still experimental. IUPAC Compendium of Chemical Terminology 2nd Edition (1997) describes a mechanism as: 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. CMLReact provides reactionScheme and annotions to describe the reaction sequence and both it and mechanism could co-occur within a reactionScheme container. 2006-02-28 PMR: changed content model to choice.