This set of tests examines the Benson Rules. There are several ways to examine the Benson Rule database:
The following command lists all the Benson Group Additivity Rulein the system:
BensonRule Listwhere:
BensonRule: The keyword for examining the Benson Group Additivity RuledatabaseList: The keyword to list all the names of the Benson Group Additivity RuleFor example, the following command:
BensonRule Listgives the output (just a snippet):
Group Additivity Rules -----------------------------------------c-(h)/3-(c)c-(c/b)(h)/3c-(c/d)(h)/3c-(h)/2-(c)/2c-(h)-(c)/3c-(c)/4c/d-(h)/2c/d-(h)-(c)c/d-(c)/2c/d-(c/d)-(h)c/d-(c/d)-(c)c/d-(c/b)-(h)c/d-(c/b)-(c)c/d-(c/t)-(h)c/d-(c/b)/2c/d-(c/d)/2c-(c/d)-(c)-(h)/2c-(c/d)/2-(h)/2c-(c/d)-(c/b)-(h)/2c-(c/t)-(c)-(h)/2c-(c/b)-(c)-(h)/2c-(c/d)-(c)/2-(h)c-(c/t)-(c)/2-(h)c-(c/b)-(c)/2-(h)c-(c/d)-(c)/3c-(c/b)-(c)/3c/t-(h)c/t-(c)c/t-(c/d)c/t-(c/b)c/b-(h)-(c/b)/2c/b-(c)-(c/b)/2c/b-(c/d)-(c/b)/2c/b-(c/t)-(c/b)/2c/b-(c/b)/3c/t-(c/t)c-(c)/3(c/t)c/bf-(c/bf)c/bf-(c/bf)/2c/bf-(c/bf)/3c-(c/b)-(c/d)-(c)-(h)co-(co)-(c)co-(o)-(c/d)co-(o)-(c/b)co-(o)-(c)co-(o)-(h)co-(c/d)-(h)co-(c/b)/2co-(c/b)-(c)co-(c)/2co-(c)-(h)co-(co)(h)o-(c/b)(co)o-(co)/2o-(co)-(o)o-(co)-(c/d)o-(co)-(c)o-(co)-(h)o-(o)-(c)o-(o)/2o-(o)-(h)o-(c/d)/2o-(c/d)-(c)o-(c/b)/2o-(c/b)-(c)o-(c/b)-(h)o-(c)/2o-(c)-(h)c/d-(co)-(o)c/d-(co)-(c)c/d-(co)-(h)c/d-(o)-(c/d)c/d-(o)-(c)c/d-(o)-(h)c/b-(co)-(c/b)/2c/b-(o)-(c/b)/2c-(co)/2-(h)/2c-(co)-(c)/2-(h)c-(co)-(c)-(h)/2c-(co)-(c)/3c-(co)-(h)/3c-(o)/2-(c)/2c-(o)/2-(c)-(h)c-(o)/2-(h)/2c-(o)-(c/b)-(h)/2c-(o)-(c/d)-(h)/2c-(o)-(c)/3c-(o)-(c)/2-(h)c-(o)-(c)-(h)/2c-(o)-(h)/3c-(o)(c/t)(h)/2o-(c/d)(h)c-(co)(c/t)(h)/2c-(co)-(c/b)-(h)/2c-(co)/2(c)(h)co-(c/t)(h)co-(c/b)(co)co-(o)/2c-(co)-(c/d)-(h)/2o-(o)-(c/d)c-(c)-(o)-(c/d)-(h)c-(c)/2-(o)-(c/d)c-(o)/2-(c/d)-(h)c-(o)/2-(c/d)-(c)c-(o)-(co)-(c)-(h)c-(o)/3-(h)c-(o)/3-(c)c-(o)/3-(c/d)c-(h)/2-(o)-(co)c-(c)-(o)/2-(co)c-(o)/2-(h)-(co)c-(h)-(c)-(c/d)2c-(h)-(c)-(c/d)-(c/t)o-(o)-(c/b)c-(h)-(c/d)2-(o)c-(c/d)-(h)-(o)-(c/b)c-(n)-(h)/3c-(n)-(c)-(h)/2c-(n)-(c)/2-(h)c-(n)-(c)/3c-(n/i)(c)(h)n-(c)-(h)/2n-(c)/2-(h)n-(c)/3n-(n)-(h)/2n-(n)-(c)-(h)n-(n)-(c)/2n-(n)-(c/b)-(h)n/i-(h)n/i-(c)n/i-(c/b)n/a-(h)n/a-(c)n-(c/b)-(h)/2n-(c/b)-(c)-(h)n-(c/b)-(c)/2n-(c/b)/2-(h)c/b-(n)-(c/b)/2c/b-('no2')-(c/b)/2n/a-(n)co-(n)-(h)co-(n)-(c)n-(co)-(h)/2n-(co)-(c)-(h)n-(co)-(c)/2n-(co)-(c/b)-(h)n-(co)/2-(h)n-(co)/2-(c)c-(cn)-(c)-(h)/2c-(cn)-(c)/2-(h)c-(cn)-(c)/3c-(cn)/2-(c)/2c/d-(cn)-(h)c/d-(cn)/2c/d-('no2')(h)c/b-(cn)-(c/b)/2c/t-(cn)c-('no2')(c)-(h)/2c-('no2')(c)/2-(h)c-('no2')/2(c)-(h)o-(no)-(c)c/b-(no)-(c/b)/2c-(c)/2-('no2')/2c-(c)('no2')/3c/d-(c)('no2')c-(n)-(c)/2-(co)n-(c/b)-(co)c-(f)/3-(c)c-(f)/2-(h)-(c)c-(f)-(h)/2-(c)c-(f)/2-(c)/2c-(f)-(h)-(c)/2c-(f)-(c)/3c-(f)/2-(cl)-(c)c-(cl)/3-(c)c-(cl)/2-(h)-(c)c-(cl)-(h)/2-(c)c-(cl)/2-(c)/2c-(cl)-(h)-(c)/2c-(cl)-(c)/3c-(br)/3-(c)c-(br)-(h)/2-(c)c-(br)-(h)-(c)/2c-(br)-(c)/3c-(i)-(h)/2-(c)c-(i)-(h)-(c)/2c-(i)-(c)/3c-(i)/2(c)(h)c-(cl)-(br)-(h)-(c)n-(f)/2-(c)c-(cl)-(c)-(o)-(h)c-(i)(o)(h)/2c/d-(c)(cl)c/d-(f)/2c/d-(cl)/2c/d-(br)/2c/d-(f)-(cl)c/d-(f)-(br)c/d-(cl)-(br)c/d-(f)-(h)c/d-(cl)-(h)c/d-(br)-(h)c/d-(i)-(h)c/t-(cl)c/t-(br)c/t-(i)c/b-(f)-(c/b)/2c/b-(cl)-(c/b)/2c/b-(br)-(c/b)/2c/b-(i)-(c/b)/2c-(c/b)-(f)/3c-(c/b)-(br)-(h)/2c-(c/b)-(i)-(h)/2co-(c/b)(cl)co-(c/b)(br)co-(c/b)(i)c-(cl)/3-(c/d)c-(h)/3-(s)c-(c)-(h)/2-(s)c-(c)/2-(h)-(s)c-(c)/3-(s)c-(c/b)-(h)/2-(s)c-(c/d)-(h)/2-(s)c/b-(s)-(c/b)/2c/d-(h)-(s)c/d-(c)-(s)s-(c)-(h)s-(c/b)-(h)s-(c)/2s-(c)-(c/d)s-(c/d)/2s-(c/b)-(c)s-(c/b)/2s-(s)-(c)s-(s)-(c/b)s-(s)/2c-(so)-(h)/3c-(c)-(so)-(h)/2c-(c)/3-(so)c-(c/d)-(so)-(h)/2c/b-(so)-(c/b)/2so-(c)/2so-(c/b)/2c-(c)-('so2')(h)/2c-(c)/2-('so2')(h)c-(c)/3-('so2')c-(c/d)-('so2')(h)/2c-(c/b)-('so2')(h)/2c/b-('so2')-(c/b)/2c/d-(h)-('so2')c/d-(c)-('so2')'so2'-(c/d)(c/b)'so2'-(c/d)/2'so2'-(c)/2'so2'-(c)(c/b)'so2'-(c/b)/2'so2'-('so2')(c/b)'so2'-(c/d)(c)co-(s)-(c)s-(h)-(co)c-(s)-(f)/3cs-(n)/2n-(cs)-(h)/2s-(s)-(n)n-(s)-(c)/2so-(n)/2n-(so)-(c)/2'so2'-(n)/2n-('so2')(c)/2c/b-('so2n3')-(c/b)/2so-(c/b)(c)c-(h)/3('so4')'so4'-(c)/2c-(h)/2(c)('so4')c-(h)/3('so3')'so3'-(c)/2c-(h)/2(c)('so3')c-(h)(c)/2('so4')c-(c)/3('so4')c-(h)(c)/2('so3')c-(c)/3('so3')c-(h)(c)/2(so)c/b-('so3h')-(c/b)/2c-(s)/2-(c)/2c-(sn)-(h)/3c-(sn)-(c)-(h)/2c-(sn)-(c)/2-(h)c-(sn)-(c)/3c-(sn)-(c/b)-(h)/2c/b-(sn)-(c/b)/2c/d-(sn)-(h)sn-(c)/4sn-(c)/3-(cl)sn-(c)/2-(cl)/2sn-(c)-(cl)/3sn-(c)/3-(br)sn-(c)/3-(i)sn-(c)/3-(h)sn-(c/d)/4sn-(c/d)/3-(cl)sn-(c/d)/2-(cl)/2sn-(c/d)-(cl)/3sn-(c)/3-(c/d)sn-(c/b)/4sn-(c)/3-(c/b)sn-(c)/3-(sn)c-(pb)-(h)/3c-(pb)-(c)-(h)/2pb-(c)/4o-(cr)-(c)cr-(o)/4c-(zn)-(h)/3c-(zn)-(c)-(h)/2zn-(c)/2o-(ti)-(c)ti-(o)/4n-(ti)-(c)/2ti-(n)/4o-(v)-(c)v-(o)/4c-(cd)-(h)/3c-(cd)-(c)-(h)/2cd-(c)/2c-(al)-(h)/3c-(al)-(c)-(h)/2al-(c)/3c-(ge)-(c)-(h)/2ge-(c)/4ge-(ge)-(c)/3c-(hg)-(h)/3c-(hg)-(c)-(h)/2c-(hg)-(c)/2-(h)c/b-(hg)-(c/b)/2hg-(c)/2hg-(c)-(cl)hg-(c)-(br)hg-(c)-(i)hg-(c/b)/2hg-(c/b)-(cl)hg-(c/b)-(br)hg-(c/b)-(i)c-(p)(h)/3c-(p)(c)(h)/2c-(po)(h)/3c-(po)(c)(h)/2c-(pn)-(h)/3c-(pn)-(c)-(h)/2c/b-(p)-(c/b)/2c/b-(po)-(c/b)/2c/b-(pn)-(c/b)/2p-(c)/3p-(c)(cl)/2p-(c/b)/3p-(o)/3p-(n)/3po-(c)/3po-(c)(f)/2po-(c)(cl)(f)po-(c)(cl)/2po-(c)(o)(cl)po-(c)(o)/2po-(o)/3po-(o)/2(f)po-(c/b)/3po-(n)/3o-(c)(p)o-(h)(p)o-(c)(po)o-(h)(po)o-(po)/2o-(pn)-(c)n-(p)(c)/2n-(po)(c)/2pn-(c)/4pn-(c/b)/3-(c)pn-(pn)/2-(c)/2pn-(pn)/2-(c/b)/2pn-(pn)/2-(cl)/2pn-(pn)/2(o)/2c-(b)(h)/3c-(b)(c)(h)/2c-(b)(c)/2(h)c-('bo3')(c)(h)/2c/d-(b)(h)b-(c)/3b-(c)(f)/2b-(c)/2(cl)b-(c)/2(br)b-(c)/2(i)b-(c)/2(o)b-(c/d)(f)/2b-(o)/3b-(o)/2(cl)b-(o)(cl)/2b-(o)/2(h)b-(n)/3b-(n)/2(cl)b-(n)(cl)/2'bo3'-(c)/3o-(b)(h)o-(b)(c)n-(b)(c)/2b-(s)/3s-(b)(c)s-(b)(c/b)c/b-(pb)-(c/b)/2pb-(c/b)/4c-(h)/3(si)si-(c)/4si-(c)(h)/3si-(c/b)/4c/b-(si)-(c/b)/2c-(h)/2(c)(si)c-(c/d)/2-(c)-(h)c-(h)/2-(c/t)/2c-(h)/2-(c/b)/2c-(h)-(c/b)/3c-(c/b)/4c-(h)-(o)-(co)-(c)c-(o)/4c-(h)-(o)/3c-(c)/2-(o)-(c/b)c-(h)/2-(n)/2c-(h)/2-(c/b)-(n)n-(h)-(c/d)/2n-(c)-(c/d)/2n-(c)-(c/b)/2n-(c/b)/3n/a-(c/b)c-(h)/2-(c)-(n/a)c-(h)-(c)/2-(n/a)c-(c)/3-(n/a)c/d-(h)-(n)c/d-(c)-(n)c/b-(n/a)-(c/b)/2c/b-(h)-(n/i)/2co-(n)/2c-(c/d)-(cn)-(h)/2c-(c/b)-('no2')-(h)/2c-(co)-(n)-(c)-(h)c-(co)-(n)-(h)/2n-(c)-('no2')/2n-(c)-(c/b)-('no2')n-(c)/2-(no)n-(c)/2-('no2')c-(s)/2-(h)/2s-(c/d)-(h)s-(s)-(h)o-(so)-(h)o-(so)-(c)so-(o)/2c-(c/d)-(c)-('so2')-(h)c-(c/t)-('so2')-(h)/2c/t-('so2')'so2'-(o)/2'so2'-(c/t)-(c/b)o-('so2')-(h)o-('so2')-(c)c-(c)-('cl')-(f)-(h)c-(c)-(cl)/2-(f)c-(c)-(br)-(f)/2c-(h)/2-(co)-(cl)c-(h)-(co)-(cl)/2co-(c)-(f)c-(c/b)-(cl)-(h)/2co-(c)-(cl)co-(c)-(br)co-(c)-(i)c-(co)-(cl)-(c)-(h)c-(h)/3-(n/a)c-(h)/3-(n/i)c-(c/t)(h)/3co-(c/b)-(h)co-(co)(o)o-(c/t)(h)co-(c/d)-(c)c-('no2')(c)/3o-('no2')(c)c-('so2')(h)/3c-('bo3')(h)/3co-(c/d)-(n)Group Additivity Rules -----------------------------------------The following command give the Benson Group Additivity rule for the element:
BensonRule Element name
where:
BensonRule: The keyword for examining the Benson Group Additivity Rule databaseElement: The keyword to retrieve the Benson Group Additivity RuleFor example, the following command:
BensonRule Element "o-(co)-(c)"gives the output:
Group Additivity Rule -----------------------------------------BensonThermodynamicBase(o-(co)-(c)): Reference: 'Benson20210129'H298: -45.13 S298: 8.61 [ 300.0, 2.82] [ 400.0, 3.79] [ 500.0, 4.38] [ 600.0, 4.73] [ 800.0, 4.91] [ 1000.0, 5.03]Group Additivity Rule -----------------------------------------The command:
BensonRuleTest Single "ch3/ch2/ch3" "c-(c)-(h)/3"where:
BensonRuleTest: the keyword for Benson Atom testsSingle: The keyword signalling the testing of a single Benson Group Additivity Ruleelementmolecule: The molecule in Nancy linear formelement: The database name of the Benson Group Additivity RuleThe output is in three parts:
For example, to test one of the primary carbon Benson Rule on propane (quotes are used around the molecule and element because of the special characters:
BensonRuleTest Single "ch3/ch2/ch3" "c-(c)-(h)/3"The output is:
Molecule -----------------------------------------------<?xml version="1.0" encoding="ISO-8859-1"?><molecule id="m1" xmlns="http://www.xml-cml.org/schema"> <atomArray> <atom id="a0" elementType="C" formalCharge="0"/> <atom id="a1" elementType="H" formalCharge="0"/> <atom id="a2" elementType="H" formalCharge="0"/> <atom id="a3" elementType="H" formalCharge="0"/> <atom id="a4" elementType="C" formalCharge="0"/> <atom id="a5" elementType="H" formalCharge="0"/> <atom id="a6" elementType="H" formalCharge="0"/> <atom id="a7" elementType="C" formalCharge="0"/> <atom id="a8" elementType="H" formalCharge="0"/> <atom id="a9" elementType="H" formalCharge="0"/> <atom id="a10" elementType="H" formalCharge="0"/> </atomArray> <bondArray> <bond id="b1" atomRefs2="a1 a0" order="S"/> <bond id="b2" atomRefs2="a2 a0" order="S"/> <bond id="b3" atomRefs2="a3 a0" order="S"/> <bond id="b4" atomRefs2="a4 a0" order="S"/> <bond id="b5" atomRefs2="a5 a4" order="S"/> <bond id="b6" atomRefs2="a6 a4" order="S"/> <bond id="b7" atomRefs2="a7 a4" order="S"/> <bond id="b8" atomRefs2="a8 a7" order="S"/> <bond id="b9" atomRefs2="a9 a7" order="S"/> <bond id="b10" atomRefs2="a10 a7" order="S"/> </bondArray></molecule>Molecule -----------------------------------------------Molecule with Benson meta atoms ------------------------------<?xml version="1.0" encoding="ISO-8859-1"?><molecule id="m1" xmlns="http://www.xml-cml.org/schema"> <atomArray> <atom id="a0" elementType="H" formalCharge="0"/> <atom id="a1" elementType="H" formalCharge="0"/> <atom id="a2" elementType="H" formalCharge="0"/> <atom id="a3" elementType="H" formalCharge="0"/> <atom id="a4" elementType="H" formalCharge="0"/> <atom id="a5" elementType="H" formalCharge="0"/> <atom id="a6" elementType="H" formalCharge="0"/> <atom id="a7" elementType="H" formalCharge="0"/> <atom id="a8" elementType="C" formalCharge="0"> <scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar> </atom> <atom id="a9" elementType="C" formalCharge="0"> <scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar> </atom> <atom id="a10" elementType="C" formalCharge="0"> <scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar> </atom> </atomArray> <bondArray> <bond id="b1" atomRefs2="a0 a8" order="S"/> <bond id="b2" atomRefs2="a1 a8" order="S"/> <bond id="b3" atomRefs2="a2 a8" order="S"/> <bond id="b4" atomRefs2="a9 a8" order="S"/> <bond id="b5" atomRefs2="a3 a9" order="S"/> <bond id="b6" atomRefs2="a4 a9" order="S"/> <bond id="b7" atomRefs2="a10 a9" order="S"/> <bond id="b8" atomRefs2="a5 a10" order="S"/> <bond id="b9" atomRefs2="a6 a10" order="S"/> <bond id="b10" atomRefs2="a7 a10" order="S"/> </bondArray></molecule>Molecule with Benson meta atoms ------------------------------Benson Group Structure ----------------------------------Benson Group: c-(c)-(h)/3 Center: c [c,1] [h,3]Benson Group Structure ----------------------------------List of Atoms applied (2)--------------------------------------a8: Ca10: CList of Atoms applied ------------------------------------------The command:
BensonRuleTest Full moleculewhere:
BensonRuleTest: the keyword for Benson Atom testsmolecule: The molecule in Nancy linear formThe output is in two parts:
For example, to test Benson Group Additivity Rule recognition of JThermodynamics on propane (quotes are used around the molecule and element because of the special characters):
BensonRuleTest Full "ch3/ch2/ch3"The output is:
Molecule -----------------------------------------------<?xml version="1.0" encoding="ISO-8859-1"?><molecule id="m1" xmlns="http://www.xml-cml.org/schema"> <atomArray> <atom id="a0" elementType="C" formalCharge="0"/> <atom id="a1" elementType="H" formalCharge="0"/> <atom id="a2" elementType="H" formalCharge="0"/> <atom id="a3" elementType="H" formalCharge="0"/> <atom id="a4" elementType="C" formalCharge="0"/> <atom id="a5" elementType="H" formalCharge="0"/> <atom id="a6" elementType="H" formalCharge="0"/> <atom id="a7" elementType="C" formalCharge="0"/> <atom id="a8" elementType="H" formalCharge="0"/> <atom id="a9" elementType="H" formalCharge="0"/> <atom id="a10" elementType="H" formalCharge="0"/> </atomArray> <bondArray> <bond id="b1" atomRefs2="a1 a0" order="S"/> <bond id="b2" atomRefs2="a2 a0" order="S"/> <bond id="b3" atomRefs2="a3 a0" order="S"/> <bond id="b4" atomRefs2="a4 a0" order="S"/> <bond id="b5" atomRefs2="a5 a4" order="S"/> <bond id="b6" atomRefs2="a6 a4" order="S"/> <bond id="b7" atomRefs2="a7 a4" order="S"/> <bond id="b8" atomRefs2="a8 a7" order="S"/> <bond id="b9" atomRefs2="a9 a7" order="S"/> <bond id="b10" atomRefs2="a10 a7" order="S"/> </bondArray></molecule>Molecule -----------------------------------------------With Benson Atoms ----------------------------------------------------------<?xml version="1.0" encoding="ISO-8859-1"?><molecule id="m1" xmlns="http://www.xml-cml.org/schema"> <atomArray> <atom id="a0" elementType="H" formalCharge="0"/> <atom id="a1" elementType="H" formalCharge="0"/> <atom id="a2" elementType="H" formalCharge="0"/> <atom id="a3" elementType="H" formalCharge="0"/> <atom id="a4" elementType="H" formalCharge="0"/> <atom id="a5" elementType="H" formalCharge="0"/> <atom id="a6" elementType="H" formalCharge="0"/> <atom id="a7" elementType="H" formalCharge="0"/> <atom id="a8" elementType="C" formalCharge="0"> <scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar> </atom> <atom id="a9" elementType="C" formalCharge="0"> <scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar> </atom> <atom id="a10" elementType="C" formalCharge="0"> <scalar dictRef="cdk:partialCharge" dataType="xsd:double">0.0</scalar> </atom> </atomArray> <bondArray> <bond id="b1" atomRefs2="a0 a8" order="S"/> <bond id="b2" atomRefs2="a1 a8" order="S"/> <bond id="b3" atomRefs2="a2 a8" order="S"/> <bond id="b4" atomRefs2="a9 a8" order="S"/> <bond id="b5" atomRefs2="a3 a9" order="S"/> <bond id="b6" atomRefs2="a4 a9" order="S"/> <bond id="b7" atomRefs2="a10 a9" order="S"/> <bond id="b8" atomRefs2="a5 a10" order="S"/> <bond id="b9" atomRefs2="a6 a10" order="S"/> <bond id="b10" atomRefs2="a7 a10" order="S"/> </bondArray></molecule>With Benson Atoms ----------------------------------------------------------Contributions ----------------------------------------------------------BensonThermodynamicBase(c-(h)/3-(c)): Reference: 'Benson20210129'H298: -10.01 S298: 30.29 [ 300.0, 7.74] [ 400.0, 9.24] [ 500.0, 10.62] [ 600.0, 12.84] [ 800.0, 14.59] [ 1000.0, 14.77] [ 1500.0, 17.58]BensonThermodynamicBase(c-(h)/2-(c)/2): Reference: 'Benson20210129'H298: -5.00 S298: 9.65 [ 300.0, 5.59] [ 400.0, 7.08] [ 500.0, 8.43] [ 600.0, 9.53] [ 800.0, 11.23] [ 1000.0, 12.48] [ 1500.0, 14.25]BensonThermodynamicBase(c-(h)/3-(c)): Reference: 'Benson20210129'H298: -10.01 S298: 30.29 [ 300.0, 7.74] [ 400.0, 9.24] [ 500.0, 10.62] [ 600.0, 12.84] [ 800.0, 14.59] [ 1000.0, 14.77] [ 1500.0, 17.58]Total ------------------------------------------------------------------BensonThermodynamicBase(Total): Reference: 'Sum Total'H298: -25.02 S298: 70.23 [ 300.0, 21.07] [ 400.0, 25.56] [ 500.0, 29.67] [ 600.0, 35.21] [ 800.0, 40.41] [ 1000.0, 42.02] [ 1500.0, 49.41]------------------------------------------------------------------------