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StoichiometryTools
byJeffreyKantor
18Dec2010(Updated06Dec2014)
Parsechemicalformulasformolecularweightsand
stoichiometricanalysis.

DownloadToolbox
DownloadZip
CodecoveredbytheBSDLicense

Highlightsfrom

StoichiometryTools
StoichTools:ToolsforDoingStoichiometry

StoichTools:ToolsforDoingStoichiometry

StoichTools:ToolsforDo...
zHW:CombusionofAmmonia...

StoichToolscomprisesasetofMatlabfunctionsfordoingstoichiometricanalysis.Thesefunctionsparsestandardchemicalnotation
foravarietyofstoichiometriccalculationsincludingfindingmolecularweights,balancingreactionsforatomandchargeconservation,
findingindependentreactions,anddisplayingformulasinHillnotation.Thefunctionsaccountforbothchangeandatomicbalancesso
theycanbeusedtobalanceionicreactionsandchemicalhalfreactions.

zHW:CompleteCombustion...

StoichToolshasextensivedocumentationincludingasetofworkedhomeworkproblemsdemonstratinguseofthefunctions.

zHW:StoichiometricMatrix

ThesefunctionsweredevelopedtosupportintroductorycoursesinChemicalEngineering.

atomic(varargin)

JeffKantor
December18,2010

ATOMICComputestheatomic
matrixforagivensetofchemical
species.

zHW:HillNotation
zHW:MultipleIndependent...

disp_reaction(V,species)

Contents
WhatisStoichTools?

DISP_REACTIONDisplays
reactionsforagivenstoichiometric
matrix.

ParsingChemicalFormulas

hillformula(varargin)

AdditionalParsingExamples
NonstoichiometricFormulas

%HILLFORMULAProduceacell
arrayofchemicalformulasinHill
Notation.

FromAtomstoChemicalFormulas

molweight(varargin)

HillNotation&CanonicalRepresentations
CreatingMolecularWeightTables

MOLWEIGHTComputesthe
molecularweightsforasetof
chemicalspecies.

AtomicMatrix

parse_formula(varargin)

AtomicMatrixforIonicSpecies

PARSE_FORMULAParsesa
chemicalformulatoformanatomic
representation.

ChemicalAbbreviationsandIsotopes

MolecularWeight

BalancingaReaction
StoichiometricMatrix
MulitpleIndependentReactions
FurtherExamplesofComplexReactions
ChemicalEquationswithIonicCharges
ChemicalHalfEquations
NestedFormulas
VersionHistory

WhatisStoichTools?

stoich(varargin)
STOICHComputesastoichiometric
matrixforasetofchemicalspecies.
Contents.m
STOICHTOOLS
cleanup.m
CleanuptheStoichToolsDirectory
Viewallfiles

StoichToolsworkswithtwotypesofdata:
1.Chemicalformulas.Eachchemicalformulaisastringwritteninanearlyuniversalchemicalnotation.Forexample,
H2SO4representsSulfuricAcid.Groupingisallowed(e.g.,CH3(CH2)6CH3foroctane)witheitherparentheses'()'or
brackets'[]'.Chargeisindicatedbyatrailing+orfollowedbyanoptionalnumber(e.g.,Fe+3orHSO4).Phase
informationmaybeincludedasaterminal(aq),(l),(g),or(s).Cellarrayscanbeusedinmostplacestoworkwith
multipleformulasatonetime(e.g.,{'H2SO4','H+','SO42'}).
2.Atomicrepresentation.Manycalculationsrequireknowledgeofthecharge,andofnumberofatomsofeachtypeina
chemicalspecies.ThisismaintainedinaMatlabstructurewherer.C,forexample,isthenumberofcarbonatoms.The
symbolafterthedotisthestandard1or2charactersymbolforanelement.ThesymbolQisreservedtoindicated
charge.AMatlabstructurearrayisusedtostoremultipleatomicreprentationsinasinglevariable.
StoichToolsprovidesfunctionsforthefollowingtypesofchemicalcalculations:
WorkingwithChemicalFormulas
r=parse_formula(s)processesachemicalformulatoproduceanatomicrepresentation.Thisfunctionismainlyusedbyother
functionstoprocesschemicalformulas.
hillformulaprocessesachemicalformulaoratomicreprentationtoproduceachemicalformulainstandardHillnotation.TheHill
notationwidelyusedtorepresentspeciesinchemicaldatabases,suchastheNISTChemistryWebbook.

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CalculatingMolecularWeights
mw=molweight(s)computesthemolecularweightsofchemicalcompounds.Inputcanbeachemicalformula,acellarrayof
chemicalformulas,oranarrayofatomicrepresentations.Ifnooutputisindicated,thenatableofmolecularweightsisprinted.
Stoichiometry
[A,atoms,species]=atomic(s)constructstheatomicmatrixforasetofchemicalcompounds.ElementA(i,j)isthenumberof
atoms{i}inspecies{j}.Inputsmaybechemicalformula,acellarrayofchemicalformulas,Ifthereareionicspecies,thenaspecial
atom'Q'isindicatesthechargeofthespecies.Ifnooutputisindicated,thentheatomicmatrixisdisplayedintabularform.
V=stoich(s)computesthestoichiometricmatrixforasetofchemicalcompounds.Theinputisacellarrayofchemicalformulas,or
anarrayofatomicrepresentations.ThecolumnsofVcorrespondtoindependentchemicalreactionssatisfyingatomicandcharge
balances.ElementV(j,k)isthestoichiometriccoefficientforspeciesjinreactionk.Anegativevaluedenotesareactant,apositive
valuedenotesaproduct.Ifnooutputisindicated,thendisp_reactionisusedtodisplayallindependentreactions.
Vout=disp_reaction(V,s)Ifnooutputisindicated,thenformatanddisplaysthechemicalreactionsdenotedbystoichiometric
matrixVandthearrayofspeciess.Thespeciesmaybecellarrayofformulasoranarrayofatomicrepresentations.Iffeasible,the
coefficientsarescaledtointegers.Itintegercoefficientsaretoolong,theneitherrationalorfloatingpointcoefficientsaredisplayed.If
anoutputisindicated,thenVoutisastoichiometricmatrixwithrescaledcoefficients,andthereactionsarenotdisplayed.
HomeworkProblemswithSolutions
TheStoichToolsfolderincludesanumberofworkedhomeworkproblems.TheseareMatlabscriptswithtitlesinthepatternHW_xx.m.
Eachscriptbeginswithacellcontainingtheproblemstatement.Subsequentcellsdemonstratesolutiontotheproblem.The
homeworkfilescanbesviewedbyusingtheMatlabpublishingfunction.

ParsingChemicalFormulas
Givenasetofchemicalspecies,r=parse_formula(s)parsesacellarrayofchemicalformulastoproduceastructurearrayr.The
valueisthenumberofatomsofthatelementpresentinthecorrespondingformula.Thestructurearrayincludesafieldforeach
atomicelementinthesetofspecies.Wecallthistheatomicrepresenationofthespecies.
%Parsingmethane
parse_formula('CH4')

ans=
C:1
H:4

AdditionalParsingExamples
ex{1}='NaHCO3';
ex{2}='KFe3(SO4)2(OH)6';%Jorosite
ex{3}='KFe3(AsO4)2(HAsO4)2';%PotassiumIronArsenate
ex{4}='(CH4)8(H2O)46';%MethaneClathrate
ex{4}='HSO4(aq)';
fork=1:length(ex)
disp(ex{k});
parse_formula(ex{k})
end

NaHCO3
ans=
Na:1
H:1
C:1
O:3
KFe3(SO4)2(OH)6
ans=
K:1
Fe:3
S:2
O:14
H:6
KFe3(AsO4)2(HAsO4)2
ans=
K:1
Fe:3
As:4
O:16
H:2

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HSO4(aq)
ans=
H:1
S:1
O:4
Q:1

ChemicalAbbreviationsandIsotopes
FormulasmayincludeD(Deuterium)orT(Tritium).Thesearetreatedaselementsandincludedasdistinctspeciesinanyatom
balances.
ThecommonorganicchemistryabbreviationsMe(Methyl,CH3),Et(Ethyl,C2H5),Bu(Butyl,C4H9),Ph(Phenol,C6H5)maybe
includedinformulas.Thesearereplacedbytheiratomicformulasduringtheparsingprocess.
ThesymbolsM(anymetal)andX(anyhalogen)maybeusedinformulas.FormulascontainingthesymbolMorXhaveunknown
molecularweight.

parse_formula('D2O')
parse_formula('EtOH')
molweight({'H2O','D2O','T2O','EtOH','PhOH','TiO2','MO2'});

ans=
D:2
O:1

ans=
C:2
H:6
O:1

SpeciesMol.Wt.

H2O18.02
D2O20.03
T2O22.03
EtOH46.07
PhOH94.11
TiO279.88
MO2NaN

NonstoichiometricFormulas
Someapplicationsofstoichiometryinvolvecomplexchemicalcompoundsnoteasilydescribedbysimplechemicalfomulas.Socalled
'nonstoichiometric'compoundscanbealsobeparsed.
bacteria='CH1.8N0.24O0.36';
parse_formula(bacteria);

FromAtomstoChemicalFormulas
Givenastructurearrayofatomicrepresentations,|s=hillformula(r)}constructsacellarrayofcorrespondingchemicalformulas.
%Formulaforoctane
octane.C=8;
octane.H=18;
hillformula(octane)

ans=
'C8H18'

HillNotation&CanonicalRepresentations
TheHillnotationisacommonlyusedsystemforwritingchemicalformulasinastandardform.%hillformula(r)producesasimple
canonicalrepresentationofachemicalspecies.Note,however,thattheremaybemanyisomersforagivenformula.
s={'Zr3B2','HBr','HCl','CH3(CH2)6CH3','NaCO3','CaC2','CH3OH',...
'CH3COOH','HNO3','H2SO4','NH3','SnH4','CH3HgCH3','(CH3CH2)4Pb',...
'[Co(NH3)6]+3','[B12H12]2'};

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fprintf('\n%15s%15s\n\n',...
'Formula','HillNotation');
fork=1:length(s)
fprintf('%15s%15s\n',s{k},char(hillformula(s{k})));
end

FormulaHillNotation

Zr3B2B2Zr3
HBrBrH
HClClH
CH3(CH2)6CH3C8H18
NaCO3CNaO3
CaC2C2Ca
CH3OHCH4O
CH3COOHC2H4O2
HNO3HNO3
H2SO4H2O4S
NH3H3N
SnH4H4Sn
CH3HgCH3C2H6Hg
(CH3CH2)4PbC8H20Pb
[Co(NH3)6]+3CoH18N6+3
[B12H12]2B12H122

MolecularWeight
mw=molweight(s)
mw=molweight(r)
Givenacellarrayofchemicalformulas,orastructurearrayofatomicrepresentations,molweightcomputesacorrespondingvector
ofmolecularweights.
%MolecularMassofDimethylMercury
s='CH3HgCH3';
mw=molweight('CH3HgCH3');
fprintf('MolecularWeightofDimethylMercury(%s)=%g\n',s,mw);

MolecularWeightofDimethylMercury(CH3HgCH3)=230.66

CreatingMolecularWeightTables
Ifmolweightasnooutput,thenitprintsatableofmolecularweights.
molweight(s);

SpeciesMol.Wt.

CH3HgCH3230.66

AtomicMatrix
[A,atoms,species]=atomic(s)
[A,atoms,species]=atomic(r)
Givenacellarrayofchemicalformulass,orastructurearrayofatomicrepresentationsr,atomiccomputestheatomicmatrixA.
atomsisaacellarrayoftheatomicelements,speciesisacellarrayofspecies.A(i,j)isthenumberofatomsofelementatoms{i}in
speciesspecies{j}.%Whencalledwithoutanoutputargument,atomicdisplaystheatomicmatrix.
s={'CH4','O2','H2O','CO2'};
atomic(s);
A=atomic(s);
disp('');
disp('A=');
disp(A);

CH4O2H2OCO2
C:1001
H:4020
O:0212

A=
1001
4020
0212

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AtomicMatrixforIonicSpecies
Forionicspeciesanadditionalrowisadded,labeledby'Q',indicatingthenetchargeoneachofthespeciesincludedinthematrix.
s={'Fe+3','SO42','H+','OH','H2O','Fe2(SO4)3'};
atomic(s);

Fe+3SO42H+OHH2OFe2(SO4)3
Fe:100002
H:001120
O:0401112
S:010003
Q:321100

BalancingaReaction
Givenacellarrayofchemicalformulas,oranarrayofatomicrepresentations,stoich(s)computesstoichiometriccoefficientsthat
satisfychargeandatombalances.Ifnooutputisspecified,thenbalancedreactionsaredisplayed.
stoich({'NaPb','CH3CH2Cl','(CH3CH2)4Pb','NaCl','Pb'});
stoich({'H+(aq)','OH(aq)','H2O(l)'});

4NaPb+4CH3CH2Cl<=>(CH3CH2)4Pb+4NaCl+3Pb

H+(aq)+OH(aq)<=>H2O(l)

StoichiometricMatrix
Givenacellarrayofchemicalformulas,orastructurearrayofatomicrepresentations,V=stoich(s)computesthestoichiometric
matrixV.V(n,r)isthestoichiometriccoeffientofspeciesninreactionr.Theatomicandstoichiometricmatricessatisfiesthe
relationshipA*V=0.
s={'C8H18','O2','C','CO','CO2','H2O'};
V=stoich(s);
disp('StoichiometricMatrixV=');
disp(V);

StoichiometricMatrixV=
100
010
001
2522
1721
900

MulitpleIndependentReactions
V=stoich(s)
disp_reaction(V,s)
ThecolumnsofthestoichiometricmatrixVrepresentindependentreactions.Thefunctiondisp_reaction(V,s)displaysthe
reactionsinaconventionalhumanreadableform.
s={'C8H18','O2','C','CO','CO2','H2O'};
V=stoich(s);
disp_reaction(V,s);

C8H18+17CO2<=>25CO+9H2O
O2+2CO<=>2CO2
C+CO2<=>2CO

FurtherExamplesofComplexReactions
Examplesfromhttp://www.chemistryhelp.net/chemistrycalculator/chemicalequationbalancer
stoich({'P2I4','P4','H2O','H3PO4','PH4I'});

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stoich({'[Cr(N2H4CO)6]4[Cr(CN)6]3','KMnO4','H2SO4','K2Cr2O7',...
'MnSO4','CO2','KNO3','K2SO4','H2O'});
stoich({'Cu(s)','HNO3(aq)','Cu(NO3)2(aq)','NO(g)','H2O(l)'});
stoich({'Cu','HNO3','H2O','Cu(NO3)2','NO'});
stoich({'KMnO4','C3H5(OH)3','K2CO3','Mn2O3','CO2','H2O'});
stoich({'K2Cr2O7','FeCl2','HCl','KCl',...
'CrCl3','FeCl3','H2O'});
stoich({'Bi(NO3)3(H2O)5','NaOH','H2O2','RuCl3',...
'NaNO3','NaCl','Bi2Ru2O7','H2O'});
stoich({'(NH4)2MoO4','NH4NO3','Na3PO4','H2O',...
'(NH4)3[P(Mo3O10)4]','NaNO3','NH3'});
stoich({'H2','Ca(CN)2','NaAlF4','FeSO4','MgSiO3','KI','H3PO4',...
'PbCrO4','BrCl','CF2Cl2','SO2','PbBr2','CrCl3','MgCO3',...
'KAl(OH)4','Fe(SCN)3','PI3','Na2SiO3','CaF2','H2O'});
stoich({'NH4ClO4','NaY(OH)4','Ru(SCN)3','PBr5','TiCl2CrI4','BeCO3',...
'Rb2ZrO3','ZnAt2','CAt2I2','Rb0.998YAt4','RuS2','BeZrO3','Zn(CN)2',...
'NaHBr1.997','H3PO4','TiCrO4','ClI','H2SO4','H2O'});

10P2I4+13P4+128H2O<=>32H3PO4+40PH4I

10[Cr(N2H4CO)6]4[Cr(CN)6]3+1176KMnO4+1399H2SO4
<=>35K2Cr2O7+1176MnSO4+420CO2+660KNO3+223K2SO4
+1879H2O

3Cu(s)+8HNO3(aq)<=>3Cu(NO3)2(aq)+2NO(g)+4H2O(l)

3Cu+8HNO3<=>4H2O+3Cu(NO3)2+2NO

14KMnO4+4C3H5(OH)3<=>7K2CO3+7Mn2O3+5CO2+16H2O

K2Cr2O7+6FeCl2+14HCl<=>2KCl+2CrCl3+6FeCl3+7H2O

2Bi(NO3)3(H2O)5+12NaOH+H2O2+2RuCl3
<=>6NaNO3+6NaCl+Bi2Ru2O7+17H2O

12(NH4)2MoO4+3NH4NO3+Na3PO4<=>12H2O+(NH4)3[P(Mo3O10)4]
+3NaNO3+24NH3

88H2+15Ca(CN)2+6NaAlF4+10FeSO4+3MgSiO3+6KI+2H3PO4
+6PbCrO4+12BrCl+3CF2Cl2+20SO2
<=>6PbBr2+6CrCl3+3MgCO3+6KAl(OH)4+10Fe(SCN)3+2PI3
+3Na2SiO3+15CaF2+79H2O

NH4ClO4+1.752NaY(OH)4+1.9188Ru(SCN)3+0.69974PBr5
+0.37423TiCl2CrI4+0.87425BeCO3+0.87425Rb2ZrO3
+3.3782ZnAt2+0.12575CAt2I2<=>1.752Rb0.998YAt4+1.9188RuS2
+0.87425BeZrO3+3.3782Zn(CN)2+1.752NaHBr1.997
+0.69974H3PO4+0.37423TiCrO4+1.7485ClI+1.9188H2SO4
+1.6596H2O

ChemicalEquationswithIonicCharges
Thechargeonionicspeciesisindicatedby+orfollowedbyanoptionaldigitindicatingtheamountofcharge.Ifionicspeciesare
present,thenachargebalanceisincludeinthecomputationofthestoichiometriccoefficients.
stoich({'ClO2+(aq)','H3O+(aq)','Cl2(g)','H2O(l)','ClO3(aq)','ClO2(aq)'});
stoich({'Bi+3(aq)','HSnO2(aq)','OH(aq)','Bi(s)','H2O','SnO32(aq)'});
stoich({'CH3CH2OH','Cr2O72','H+','CH3COOH','Cr+3','H2O'});
stoich({'I','I2','Mn+2','MnO4','H+','H2O'});
stoich({'Cl2','Cl','Fe+2','Fe+3'});
stoich({'Mn+2','BiO3','H+','MnO4','Bi3+','H2O'});
stoich({'NpO2+2','NpO2(OH)H2C2O4+','NpO2+','CO2','H+','O2'});
stoich({'H3PO4','(NH4)6Mo7O24','H+','(NH4)3PO4(MoO3)12','NH4+','H2O'});

4ClO2+(aq)+Cl2(g)+4ClO3(aq)<=>10ClO2(aq)
8H3O+(aq)+Cl2(g)+8ClO3(aq)<=>12H2O(l)+10ClO2(aq)

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2Bi+3(aq)+3HSnO2(aq)+9OH(aq)<=>2Bi(s)+6H2O
+3SnO32(aq)

3CH3CH2OH+2Cr2O72+16H+<=>3CH3COOH+4Cr+3+11H2O

10I+2MnO4+16H+<=>5I2+2Mn+2+8H2O

Cl2+2Fe+2<=>2Cl+2Fe+3

4Mn+2+5Bi3++31H2O<=>15BiO3+62H++4MnO4

6NpO2+2+2NpO2(OH)H2C2O4+<=>8NpO2++4CO2+6H++O2

7H3PO4+12(NH4)6Mo7O24+51H+<=>7(NH4)3PO4(MoO3)12+51NH4+
+36H2O

ChemicalHalfEquations
Includethebareelectron'e'tobalancechemicalhalfreactions.Inacidicsolutions,ifoneofthemainreactantscontainsoxygen,add
'H+'and'H2O'.Inbasicsolutions,ifoneofthemainreactantscontainsoxygenthenadd'OH'and'H2O'.
stoich({'Al+3(aq)','Al(s)','e'});
stoich({'Cl(aq)','Cl2(g)','e'});
%AcidicSolutions
stoich({'MnO4(aq)','Mn+2(aq)','H2O(l)','H+(aq)','e'});
stoich({'O2(g)','H2O(l)','H+(aq)','e'});
stoich({'Ag2O3','Ag+','H2O','H+','e'});
stoich({'S2O32(aq)','S(s)','H2O(l)','H+(aq)','e'});
stoich({'HOOCCOOH(aq)','CO2(g)','H2O(l)','H+(aq)','e'});
%AlkaliSolutions
stoich({'MnO4(aq)','Mn+2(aq)','H2O(l)','OH(aq)','e'});
stoich({'Cr(OH)62','CrO42','H2O','OH','e'});
stoich({'NH3OH(aq)','N2(g)','H2O(l)','OH(aq)','e'});
stoich({'Al(OH)4(aq)','Al(s)','H2O(l)','OH(aq)','e'});
stoich({'ZrO(OH)2','Zr','H2O','OH','e'});

Al+3(aq)+3e<=>Al(s)

2Cl(aq)<=>Cl2(g)+2e

MnO4(aq)+8H+(aq)+5e<=>Mn+2(aq)+4H2O(l)

O2(g)+4H+(aq)+4e<=>2H2O(l)

Ag2O3+6H++4e<=>2Ag++3H2O

S2O32(aq)+6H+(aq)+4e<=>2S(s)+3H2O(l)

HOOCCOOH(aq)<=>2CO2(g)+2H+(aq)+2e

MnO4(aq)+4H2O(l)+5e<=>Mn+2(aq)+8OH(aq)

Cr(OH)62+2OH<=>CrO42+4H2O+2e

2NH3OH(aq)+4OH(aq)<=>N2(g)+6H2O(l)+4e

Al(OH)4(aq)+3e<=>Al(s)+4OH(aq)

ZrO(OH)2+H2O+4e<=>Zr+4OH

NestedFormulas

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Matlabregularexpressionscapabilitiesareusedtoparsechemicalformulas.WhilethiskeepsStoichToolssimpleandfast,oneofthe
drawbacksofregularexpressionsisthedifficultyofmatchingnestedexpressions.Thusnestingislimitedtobracketedexpressions
insideofparentheses,orparenthesesinsideofbrackets.Bythisrule,[Fe2(SO4)3]and(Fe2[SO4]3)areallowed,but(Fe2(SO4)3)
and[Fe2[SO4]3]arenot.Inpractice,chemicalformulararelyneedmorethantwolevelsofnesting.
disp('Theseworkfine.');
molweight({'[Fe2(SO4)3]','(Fe2[SO4]3)'});
fprintf('\n\n');
try
molweight({'(Fe2(SO4)3)','[Fe2[SO4]3]'})
catchexception
disp('Butthisdoesnot.');
disp(exception.message);
end

Theseworkfine.
SpeciesMol.Wt.

[Fe2(SO4)3]399.88
(Fe2[SO4]3)399.88

Butthisdoesnot.
Couldnotparseformula:
(Fe2(SO4)3)
^

VersionHistory
2010/12/18SubmittedtoMatlabCentral
2010/12/19Updateddocumentation,addedsolvedhomeworks
2010/12/19PutrowsoftheatomicmatrixinHillorder
2010/12/19Expandedregularexpressionparsingtoincludephases
2010/12/20Enhancedparsertoacceptnonstoichiometricformulas
2010/12/20Enhanceddisp_reactionforbettercoefficientformatting
2010/12/21ParsertoincludecommonsymbolsD,T,Et,Me,Bu,Ph
2010/12/30Fixedallmlintmessages,reducedMcCabecomplexity
2010/12/30UpdatetoMatlabCentral
2010/12/30Furtherimprovementstoerrorhandling(assert's)
2010/12/31FixedbugwithNaNinmolweight
2010/12/31RenamedhomeworkfilessoitmakesmoresenseonMC
2010/12/31UpdatetoMatlabCentral
ToDo's
AddGeneration/ConsumptionAnalysis
AddExtentofReactionAnalysis
Includeanelectrochemistryhoweworkexample(battery?)
Addadisplayfeatureforstoich
Addwebbooklookupforchemicalpropertydata

PublishedwithMATLAB7.11

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