MolecularDescriptorsGuide

DescriptionoftheMolecularDescriptorsAppearingintheToxicity

EstimationSoftwareTool

Version1.0.2

2008U.S.EnvironmentalProtectionAgency

TableofContents

I.
II.
III.
IV.
V.
VI.
VII.
VIII.
IX.
X.
XI.
XII.
XIII.
XIV.

Page

11

16

19

23

25

31

33

37

40

45

47

ConstitutionalDescriptors
ChiConnectivityIndices
KappaShapeIndices
ElectrotopologicalStateIndices
TopologicalDescriptors
MolecularFragments
2DMolecularProperties
InformationIndices
MolecularDistanceEdgeVector
Burdeneigenvaluedescriptors
WalkandPathCounts
2DAutocorrelationDescriptors
MolecularProperties
References

I. ConstitutionalDescriptors(45)

1. Molecularweight(MW)
2. SumofatomicvanderWaalsvolumes
(scaledonCarbonatom)(Sv)
3. SumofatomicSanderson
electronegativities(scaledonCarbon
atom)(Se)
4. Sumofatomicpolarizabilities(scaled
onCarbonatom)(Sp)
5. SumofKierHallelectrotopological
states(Ss)
6. Averagemolecularweight(AMW)
7. MeanatomicvanderWaalsvolume
(scaledonCarbonatom)(Mv)
8. MeanatomicSanderson
electronegativity(scaledonCarbon
atom)(Me)
9. Meanatomicpolarizability(scaledon
Carbonatom)(Mp)
10.Meanelectrotopologicalstate(Ms)
11.Numberofatoms(nAT)
12.NumberofnonHatoms(nSK)
13.Numberofbonds(nBT)
14.NumberofnonHbonds(nBO)
15.Numberofmultiplebonds(nBM)
16.Sumofconventionalbondorders(H
depleted)(SCBO)
17.Aromaticratio(ARR)
18.Numberofrings(nCIC)

19.Numberofcircuits(nCIR)
20.Numberofdoublebonds(nDB)
21.Numberoftriplebonds(nTB)
22.Numberofaromaticbonds(nAB)
23.NumberofHydrogenatoms(nH)
24.NumberofCarbonatoms(nC)
25.NumberofNitrogenatoms(nN)
26.NumberofOxygenatoms(nO)
27.NumberofPhosphorousatoms(nP)
28.NumberofSulfuratoms(nS)
29.NumberofFluorineatoms(nF)
30.NumberofChlorineatoms(nCL)
31.NumberofBromineatoms(nBR)
32.NumberofIodineatoms(nI)
33.NumberofBoronatoms(nB)
34.Numberofhalogenatoms(nX)
35.Numberof3memberedrings(nR03)
36.Numberof4memberedrings(nR04)
37.Numberof5memberedrings(nR05)
38.Numberof6memberedrings(nR06)
39.Numberof7memberedrings(nR07)
40.Numberof8memberedrings(nR08)
41.Numberof9memberedrings(nR09)
42.Numberof10memberedrings(nR10)
43.Numberof11memberedrings(nR11)
44.Numberof12memberedrings(nR12)
45.Numberofbenzenelikerings(nBnz)

Themolecularweight(MW)isthesumofthemolecularweightsoftheindividualatoms:
A

MW
=
MWi

(1)

(2)

i =1

SimilarlythesumofthevanderWaalsvolumesisgivenby

Sv
=
Vi

i =1

Thesumoftheelectronegativities(Se),polarizabilities(Sp),andKierHallelectrotopological
states(Ss)aregivenbyasimilarformulatoequation2.

Theaveragemolecularweightisgivenasfollows:

AMW = MW / nAT

(3)

wherenATisthenumberofatoms.

Themeanvolume(Mv)iscalculatedbydividingthesumofthevanderWaalsvolumesbythe
numberofatoms:
Mv = Sv / nAT
(4)

Themeanelectronegativity(Me)andmeanpolarizability(Mp)arecalculatedusingformulas
similartoequation4.

Themeanelectrotopologicalstate(Ms)iscalculatedbydividingSsbythenumberofnon
hydrogenatoms(nSK):
Ms = Ss / nSK
(5)

Thenumberofbonds(nBT)isthetotalnumberofbonds(doubleandtriplebondsarecountedas
twoandthreebonds,respectively).

ThenumberofnonHbonds(nBO)isthenumberofbondsthatdonotinvolvehydrogenatoms.

Thenumberofmultiplebonds(nBM)isthenumberofbondsthathaveabondordergreaterthan
one(note:aromaticbondshaveabondorderof1.5).

Thesumoftheconventionalbondorders(SCBO)isthesumofthebondordersofbondsnot
involvinghydrogens(againaromaticbondshaveanorderof1.5).

Thearomaticratio(ARR)isthefractionofaromaticatomsinthehydrogensuppressedgraph.

Thenumberofrings(nCIC)isthenumberofsimpleringsinthemoleculesthatarentcycles.
Thenumberofringscanbedeterminedby
nCIC = nBO nSK + 1
(6)

Thenumberofcircuits(nCIR)includesbothringsandcircuits(acircuitisalargerlooparound
twoormorerings).Asanexamplenaphthalenecontains3circuitsand2rings.

Thenumberofdoublebonds(nDB)isequaltothenumberofnonaromaticdoublebonds.

Thenumberoftriplebonds(nTB)issimplythecountoftriplebondsinthemolecule.

Thenumberofaromaticbonds(nAB)isthenumberofbondswithabondorderof1.5.

Thenumberofhydrogen(nH),carbon(nC),nitrogen(nN),oxygen(nO),phosphorus(nP),sulfur
(nS),fluorine(nF),chlorine(nCl),bromine(nBr),iodine(nI),andboron(nB)atomsaresimply
thetotalnumberofeachofthesetypesofatomsinthemolecule.

Thenumberofhalogenatomsisthesimplythesumofthecountsofthehalogenatoms:
nX = nF + nCL + nBR + nI
(7)


Thenumberoftheringsofeachsize(nR03,nR04nR12)isthecountofallthecycleswiththe
givennumberofatoms.

Thenumberofbenzenelikerings(nBnz)isthenumberofsixmemberedaromaticrings
containingnoheteroatoms.

II.ChiConnectivityIndices(46)

A.Simple

1. Simplezeroorderchiindex(0orx0)
2. Simple1storderchiindex(1orx1)
3. Simple2ndorderchiindex(2orx2)
4. Simple3rdorderpathchiindex(3porxp3)
5. Simple4thorderpathchiindex(4porxp4)
6. Simple5thorderpathchiindex(5porxp5)
7. Simple6thorderpathchiindex(6porxp6)
8. Simple7thorderpathchiindex(7porxp7)
9. Simple8thorderpathchiindex(8porxp8)
10.Simple9thorderpathchiindex(9porxp9)
11.Simple10thorderpathchiindex(10porxp10)
12.Simple3rdorderclusterchiindex(3corxc3)
13.Simple4thorderclusterchiindex(4corxc4)
14.Simple4thorderpath/clusterchiindex(4pcorxpc4)
15.Simple3rdorderchainchiindex(3chorxch3)
16.Simple4thorderchainchiindex(4chorxch4)
17.Simple5thorderchainchiindex(5chorxch5)
18.Simple6thorderchainchiindex(6chorxch6)
19.Simple7thorderchainchiindex(7chorxch7)
20.Simple8thorderchainchiindex(8chorxch8)
21.Simple9thorderchainchiindex(9chorxch9)
22.Simple10thorderchainchiindex(10chorxch10)
23.Differencebetweenchicluster3andchipath/cluster4(knotp)

Thegeneralformulaforthesimplechiconnectivityindices(mtorxtm)isasfollows:
A

t = m ci

(1)

i=1

wherem=bondorder(0=atoms,1=fragmentsofonebond,2=fragmentsoftwobonds,etc.),
t=typeofcalculation(p=path,c=cluster,pc=path/cluster,ch=chainorcycle)andA=the
numberofnonhydrogenatomsinthemolecule.Forthefirstthreepathindices(x0,x1,andx2),
thecalculationtype,p,isomittedfromthevariablenamesusedinthesoftware.

m
ci iscalculatedforallofthefragmentsoftypetandpathlengthminthehydrogendepleted
graphofthemolecule:
m

m+1

ci = ( k )

0.5

(2)

k =1

wherek=thedifferentatomsinthefragmentand k isthevertexdegreeofanatomgivenby

k = k hk

(3)

where k isthenumberofelectronsinsigmaorbitalsand hk isthenumberofbondedhydrogen

atoms(Simply k isthe#ofnonhydrogenatomsbondedtoatomk).

knotpissimplythedifferencebetweenxc3andxpc4:
knotp = xc3 xpc4

Thesimplechiindicesaredescribedonpage85oftheHandbookofMolecularDescriptors
(TodeschiniandConsonni2000).

(4)

B.Valence

1. Valencezeroorderchiindex(0vorxv0)
2. Valence1storderchiindex(1vorxv1)
3. Valence2ndorderchiindex(2vorxv2)
4. Valence3rdorderpathchiindex(3vporxvp3)
5. Valence4thorderpathchiindex(4vporxvp4)
6. Valence5thorderpathchiindex(5vporxvp5)
7. Valence6thorderpathchiindex(6vporxvp6)
8. Valence7thorderpathchiindex(7vporxvp7)
9. Valence8thorderpathchiindex(8vporxvp8)
10.Valence9thorderpathchiindex(9vporxvp9)
11.Valence10thorderpathchiindex(10vporxvp10)
12.Valence3rdorderclusterchiindex(3vcorxvc3)
13.Valence4thorderclusterchiindex(4vcorxvc4)
14.Valence4thorderpath/clusterchiindex(4vpcorxvpc4)
15.Valence3rdorderchainchiindex(3vchorxvch3)
16.Valence4thorderchainchiindex(4vchorxvch4)
17.Valence5thorderchainchiindex(5vchorxvch5)
18.Valence6thorderchainchiindex(6vchorxvch6)
19.Valence7thorderchainchiindex(7vchorxvch7)
20.Valence8thorderchainchiindex(8vchorxvch8)
21.Valence9thorderchainchiindex(9vchorxvch9)
22.Valence10thorderchainchiindex(10vchorxvch10)
23.Differencebetweenchivalencecluster3andchivalencepath/cluster4(knotpv)

Thevalenceconnectivityindices(mvtorxvtm)arecalculatedinthesamefashionasthesimple
connectivityindicesexceptthatthevertexdegreeinequationB2isreplacedbythevalence
vertexdegree(v)togive
m

( )

m+1

ci = kv
k =1

0.5

(5)

wherethevalencevertexdegreeisgivenby

kv = Z kv hk = k + k + nk hk
(6)
where Z kv isthenumberofvalenceelectrons, k =numberofelectronsinpiorbitals,and nk is
thenumberofelectronsinlonepairorbitals.

Foratomsofhigherprincipalquantumlevels,thevalencevertexdegreeisgivenby
kv = ( Z kv hk ) /( Z k Z kv 1)

(7)

where Z k isthenumberofelectronsinatomk(theatomicnumber).

Thevalencechiindicesaredescribedonpage86oftheHandbookofMolecularDescriptors
(TodeschiniandConsonni2000).Thechiconnectivityindicesaredescribedinfurtherdetailin
theliterature(Elsevier_MDL2006;HallandKier1991,1999;KierandHall1976,1986).

III.KappaShapeIndices(7)

Firstorderkappashapeindex(1ork1)
Secondorderkappashapeindex(2ork2)
Thirdorderkappashapeindex(3ork3)
Firstorderkappaalphashapeindex(1orka1)
Secondorderkappaalphashapeindex(2orka2)
Thirdorderkappaalphashapeindex(3orka3)
Kappaflexibilityindex(phia)

Thefirstorderkappashapeindex(1ork1)isgivenby

2
A( A 1)
1
=

(1)
2
1
P
whereiP=#ofpathsofbondlengthiinthehydrogensuppressedmoleculeandAisthenumber
ofnonhydrogenatomsinthemolecule.

Thesecondorderkappashapeindex(2ork2)isgivenby
( A 1)( A 2 )2
2
=

(2)
2
2
P

Thethirdorderkappashapeindex(3ork3)isgivenby
2
A 1)( A 3)
(
3
=
ifAisodd

(3)
2
3
P
1.
2.
3.
4.
5.
6.
7.

( )

( )

( )

2
A 3)( A 2 )
(
=

( P)
3

ifAiseven

(4)

Thekappashapeindicesaredescribedonpage248oftheHandbookofMoleculardescriptors
(TodeschiniandConsonni2000).

Thefirstorderkappaalphashapeindex(1orka1)isgivenby
2
A + )( A + 1)
(
1
=

(5)
2
1
P +
where
r
= 1 x

(6)
rx(sp 3 )

whererxisthecovalentradiusoftheatombeingevaluatedand rx ( sp3 ) isthecovalentradiusofa

carbonsp3atom(0.77).

Thecovalentradiiusedinthesoftwareareasfollows:

Atom/Hybrid
R()
Atom/Hybrid
R()
3
0.77
F
0.72
Csp
Csp2
0.67
Cl
0.99
Csp
0.60
Br
1.14
Nsp3
0.74
I
1.33
2
Nsp
0.62

Nsp
0.55
Si
1.17
Osp3
0.74
As
1.22
2
Osp
0.62
Sn
1.42
Psp3
1.10

2
Psp
1.00
Hg
1.48
Ssp3
1.04
Pb
1.54
2
Ssp
0.94

Thesecondorderkappaalphashapeindex(2orka2)isgivenby
( A + 1)( A + 2)2
2
=
2
2
P +

Thethirdorderkappaalphashapeindex(3orka3)isgivenby
( A + 1)( A + 3)2 ifAisodd
3
=
2
3
P +

2
A + 3)( A + 2 )
(
=

( P +)

ifAiseven

(7)

(8)

(9)

Thekappashapeindicesaredescribedonpage250oftheHandbookofMolecularDescriptors
(TodeschiniandConsonni2000).

Thekappaflexibilityindex(phia)isgivenby

phia =

(10)
A
Thekappaflexibilityindexisdescribedonpage178oftheHandbookofMolecularDescriptors
(TodeschiniandConsonni2000).

10

IV.ElectrotopologicalStateIndices(166)

A.AtomTypeEStateSumNonhydrogenIndices

1. Sumof(CH3)EStates(SsCH3)
2. Sumof(=CH2)EStates(SdCH2)
3. Sumof(CH2)EStates(SssCH2)
4. Sumof(tCH)EStates(StCH)
5. Sumof(=CH)EStates(SdsCH)
6. Sumof(aaCH)EStates(SaaCH)
7. Sumof(>CH)EStates(SsssCH)
8. Sumof(=C=)EStates(SddC)
9. Sumof(tC)EStates(StsC)
10.Sumof(=C<)EStates(SdssC)
11.Sumof(saaC)EStates (SsaaC)
12.Sumof(aaaC)EStates(SaaaC)
13.Sumof(>C<)EStates (SssssC)
14.Sumof(NH2)EStates(SsNH2)
15.Sumof(=NH)EStates(SdNH)
16.Sumof(NH)EStates(SssNH)
17.Sum of(aaNH)EStates(SaaNH)
18.Sum of(tN)EStates (StN)
19.Sum of(=N )EStates (SdsN)
20. Sum of(aaN )EStates (SaaN)
21. Sum of(>N )EStates (SsssN)
22. Sum of ( aaaN ) EStates (SaaaN)
23. Sum of ( saaN ) EStates (SsaaN)
24. Sum of ( NH3+ ) EStates (SsNH3p)
25. Sum of ( NH2+ ) EStates

(SssNH2p)

26. Sum of ( > NH+ ) EStates (SsssNHp)

27. Sum of ( = N+ = ) EStates (SddNp)
28. Sum of ( # N+ ) EStates (StsNp)
29. Sum of ( = N ) EStates (SdNm)
30. Sum of ( = N+ < ) EStates (SdssNp)
31. Sum of ( > N+ < ) EStates (SssssNp)
32. Sum of ( saaN+ ) EStates (SsaaNp)
33. Sum of ( OH ) EStates (SsOH)
34. Sum of ( = O ) EStates (SdO)
35. Sum of ( O ) EStates (SssO)
36. Sum of ( aaO ) EStates (SaaO)
37. Sum of ( O ) EStates (SsOm)
38. Sum of ( F ) EStates (SsF)

11

39. Sum of ( Cl ) EStates (SsCl)

40. Sum of ( Br ) EStates (SsBr)
41. Sum of ( I ) EStates (SsI)
42. Sum of ( SiH3 ) EStates (SsSiH3)
43. Sum of ( SiH2 ) EStates (SssSiH2)
44. Sum of ( > SiH ) EStates (SsssSiH)
45. Sum of ( > Si < ) EStates (SssssSi)
46. Sum of ( > P ) EStates (SsssP)
47. Sum of (dsssP ) EStates (SdsssP)
48. Sum of (ddsP ) EStates (SddsP)
49. Sum of ( sssssP ) EStates (SsssssP)
50. Sum of ( =PH< ) EStates (SdssPH)
51. Sum of ( PH2 ) EStates (SsPH2)
52. Sum of ( PH ) EStates (SssPH)
53. Sum of ( SH ) EStates (SsSH)
54. Sum of ( = S ) EStates (SdS)
55. Sum of ( S ) EStates (SssS)
56. Sum of ( aaS ) EStates (SaaS)
57. Sum of ( = S < ) EStates (SdssS)
58. Sum of ( ddssS ) EStates (SddssS)
59. Sum of ( ssssssS ) EStates (SssssssS)
60. Sum of ( SnH3 ) EStates (SsSnH3)
61. Sum of ( SnH2 ) EStates (SssSnH2)
62. Sum of ( > SnH ) EStates (SssSnH)
63. Sum of ( > Sn < ) EStates (SssssSn)
64. Sum of ( PbH3 ) EStates (SsPbH3)
65. Sum of ( PbH2 ) EStates (SssPbH2)
66. Sum of ( > PbH ) EStates (SsssPbH)
67. Sum of ( > Pb < ) EStates (SssssPb)
68. Sum of ( As < ) EStates (SsssAs)
69. Sum of ( dsssAs ) EStates (SdsssAs)
70. Sum of ( ddsAs ) EStates (SddsAs)
71. Sum of ( sssssAs ) EStates (SsssssAs)
72. Sumof(AsH2)EStates(SsAsH2)
73.Sumof(AsH)EStates(SssAsH)
74.Sumof(Hg+)EStates(SsHgp)
75.Sumof(Hg)EStates(SssHg)
76.Sumof(Hg)EStates(SsHg)

TheEStatevalueforagivennonhydrogenatomiinamoleculeisgivenbyitsintrinsicstate(Ii)
plusthesumoftheperturbationsonthatatombyalltheotheratomsinthemolecule:
A

S k = I k + I ki

(1)

(2)

i =1

wheretheintrinsicstate(Ik)isgivenby

Ik =

(2 / N )2 kv + 1
k

whereN=principalquantumnumber(whichisequaltotheelementsperiodorrowinthe
periodictable)where kv iscalculatedusingequation6fromSectionII(evenforelementswith
higherprincipalquantumlevels).

Theperturbationofatomkduetoatomiisgivenby
(I I )

I ki = i 2 k

(4)
rki
where
rki = d ki + 1
(5)

wheredki=isthenumberofbondsthatseparateatomkfromatomi.

Theatomtypenonhydrogenindices(SX)areobtainedbysummingtheEStatevaluesforallthe
atomsofagiventypetthatarepresentinthemolecule:

SX = S(t)
(6)
whereS(t)istheatomEStatevalue(obtainedfromequation1)foranatomoftypet.

Forexample,forpropane,theEStatesfortheindividualatomsareasfollows:

S(2)=1.25

CH3
H3 C

S(1)=2.125
S(3)=2.125

SsCH3(thesumoftheEStatesforcarbonatomswiththreehydrogensattachedandonesingle
bondtoanonhydrogenatom)is4.25(22.125).SssCH2(thesumoftheEStatesforcarbon
atomswithtwohydrogensattachedandtwosinglebondstoanonhydrogenatoms)is1.25.

12

B.AtomTypeCountNonhydrogenIndices

1. Countof(CH3)(SsCH3_acnt)
2. Countof(=CH2)(SdCH2_acnt)
3. Countof(CH2)(SssCH2_acnt)
4. Countof(tCH)(StCH_acnt)
5. Countof(=CH)(SdsCH_acnt)
6. Countof(aaCH)(SaaCH_acnt)
7. Countof(>CH)(SsssCH_acnt)
8. Countof(=C=)(SddC_acnt)
9. Countof(tC)(StsC_acnt)
10.Countof(=C<)(SdssC_acnt)
11.Countof(saaC)(SsaaC_acnt)
12.Countof(aaaC)(SaaaC_acnt)
13.Countof(>C<)(SssssC_acnt)
14.Countof(NH2)(SsNH2_acnt)
15.Countof(=NH)(SdNH_acnt)
16.Countof(NH)(SssNH_acnt)
17.Countof(aaNH)(SaaNH_acnt)
18.Countof(tN)(StN_acnt)
19.Countof(=N)(SdsN_acnt)
20.Countof(aaN)(SaaN_acnt)
21.Countof(>N)(SsssN_acnt)
22.Countof(aaaN)(SaaaN_acnt)
23.Countof(saaN)(SsaaN_acnt)
24.Countof(NH3+)(SsNH3p_acnt)
25.Countof(NH2+)(SssNH2p_acnt)
26.Countof(>NH+)(SsssNHp_acnt)
27.Countof(=N+=)(SddNp_acnt)
28.Countof(#N+)(StsNp_acnt)
29.Countof(=N)(SdNm_acnt)
30.Countof(=N+<)(SdssNp_acnt)
31.Countof(>N+<)(SssssNp_acnt)
32.Countof(saaN+)(SsaaNp_acnt)
33.Countof(OH)(SsOH_acnt)
34.Countof(=O)(SdO_acnt)
35.Countof(O)(SssO_acnt)
36.Countof(aaO)(SaaO_acnt)
37.Countof(O)(SsOm_acnt)
38.Countof(F)(SsF_acnt)

39.Countof(Cl)(SsCl_acnt)
40.Countof(Br)(SsBr_acnt)
41.Countof(I)(SsI_acnt)
42.Countof(SiH3)(SsSiH3_acnt)
43.Countof(SiH2)(SssSiH2_acnt)
44.Countof(>SiH)(SsssSiH_acnt)
45.Countof(>Si<)(SssssSi_acnt)
46.Countof(>P)(SsssP_acnt)
47.Countof(dsssP)(SdsssP_acnt)
48.Countof(ddsP)(SddsP_acnt)
49.Countof(sssssP)(SsssssP_acnt)
50.Countof(=PH<)(SdssPH_acnt)
51.Countof(PH2)(SsPH2_acnt)
52.Countof(PH)(SssPH_acnt)
53.Countof(SH)(SsSH_acnt)
54.Countof(=S)(SdS_acnt)
55.Countof(S)(SssS_acnt)
56.Countof(aaS)(SaaS_acnt)
57.Countof(=S<)(SdssS_acnt)
58.Countof(ddssS)(SddssS_acnt)
59.Countof(ssssssS)(SssssssS_acnt)
60.Countof(SnH3)(SsSnH3_acnt)
61.Countof(SnH2)(SssSnH2_acnt)
62.Countof(>SnH)(SssSnH_acnt)
63.Countof(>Sn<)(SssssSn_acnt)
64.Countof(PbH3)(SsPbH3_acnt)
65.Countof(PbH2)(SssPbH2_acnt)
66.Countof(>PbH)(SsssPbH_acnt)
67.Countof(>Pb<)(SssssPb_acnt)
68.Countof(As<)(SsssAs_acnt)
69.Countof(dsssAs)(SdsssAs_acnt)
70.Countof(ddsAs)(SddsAs_acnt)
71.Countof(sssssAs)(SsssssAs_acnt)
72.Countof(AsH2)(SsAsH2_acnt)
73.Countof(AsH)(SssAsH_acnt)
74.Countof(Hg+)(SsHgp_acnt)
75.Countof(Hg)(SssHg_acnt)
76.Countof(Hg)(SsHg_acnt)

Theatomtypecountnonhydrogenindicesaresimplythecountofeachtypeofestatefragment
withinamolecule.Forthepropaneexample,SsCH3_acnt(thecountofallCH3groupsin
molecule)is2andSssCH2_acnt(thecountofallCH2groupsinamolecule)is1.

13

C.HydrogenIndices

1.
2.
3.
4.
5.
6.
7.
8.

Sumof([OH])hydrogenEStates(SHsOH)
Sumof([=NH])hydrogenEStates(SHdNH)
Sumof([SH])hydrogenEStates(SHsSH)
Sumof([NH2])hydrogenEStates(SHsNH2)
Sumof([NH])hydrogenEStates(SHssNH)
Sumof([tCH])hydrogenEStates(SHtCH)
Sumof(CHorCH2withForClattached)hydrogenEStatevalues(SHCHnX)
SumofhydrogenEStatevaluesforotheratomtypes(SHother)

Thehydrogenelectrotopologicalstateindex( HS i )foratomnumberiisgivenby
KHE j KHE(H i )
HS i = KHE i + (KHE i KHE(H i ) ) + j i

(7)
(d ij + 1)2
whereKHEiistheKierHallelectronegativityoftheithheavyatomintheHdepletedgraph,
KHE(H i ) istheKierHallelectronegativityoftheattachedhydrogenatom(takentobe0.2),
anddijisthedistancebetweeneachjheavyatomandtheithheavyatomtowhichthehydrogen
isbonded.TheKierHallelectronegativityofagivenatomisgivenby
v
KHE i = i 2 i

(8)
Ni
whereinthiscase iv isthevalencevertexdegreegiveninequation6ofSectionIIandNiisthe
principalquantumnumberofatomi.

SHsOHisthesumofthehydrogenEStatesfortheatomswithanEStatetypeofSsOH.

SHdNHisthesumofthehydrogenEStatesfortheatomswithanEStatetypeofSdNH.

SHsSHisthesumofthehydrogenEStatesfortheatomswithanEStatetypeofSsSH.

SHsNH2isthesumofthehydrogenEStatesfortheatomswithanEStatetypeofSsNH2.

SHssNHisthesumofthehydrogenEStatesfortheatomswithanEStatetypeofSssNHor
SaaNH.

SHtCHisthesumofthehydrogenEStatesfortheatomswithanEStatetypeofStCH.

SHCHnXisthesumofthehydrogenEStatesfortheatomswithanEStatetypeofSsCH3,
SssCH2,SsssCH,orSdsCHwhenthereisachlorineorfluorineatomattached.

SHotheristhesumofthehydrogenEStatesforatoms(thathavehydrogensattached)thatdonot
fallintotheotherhydrogenEStatetypeslistedabove.

14

D.MaximumandMinimumValues

1.
2.
3.
4.
5.
6.

MaximumhydrogenEStatevalueinmolecule(Hmax)
MaximumEStatevalueinmolecule(Gmax)
MinimumhydrogenEStatevalueinmolecule(Hmin)
MinimumEStatevalueinmolecule(Gmin)
MaximumpositivehydrogenEStatevalueinmolecule.(Hmaxpos)
MinimumnegativehydrogenEStatevalueinmolecule.(Hminneg)

HmaxisthemaximumhydrogenEstatevalue(calculatedusingequation7)foralltheatomsin
themolecule.

GmaxisthemaximumEstatevalue(calculatedusingequation1)foralltheatomsinthe
molecule.

HministheminimumhydrogenEstatevalueforalltheatomsinthemolecule.

GministheminimumEstatevalueforalltheatomsinthemolecule.

HmaxposisthemaximumpositivehydrogenEstatevalueforalltheatomsinthemolecule.

HminnegistheminimumnegativehydrogenEstatevalueforalltheatomsinthemolecule.

ThecalculationofEstatesindicesisdescribedinfurtherdetailbyKierandHall(KierandHall

1999).

15

V.Topologicaldescriptors(15)

1.
FirstZagrebindexweightedbyvertexdegrees(ZM1)
2.
FirstZagrebindexweightedbyvalencevertexdegrees(ZM1V)
3.
SecondZagrebindexweightedbyvertexdegrees(ZM2)
4.
SecondZagrebindexweightedbyvalencevertexdegrees(ZM2V)
5.
Balabandistanceconnectivityindex(J)
6.
Jtindex(Jt)
7.
Balabancentricindex(BAC)
8.
Loppingcentricindex(Lop)
9.
Radialcentricinformationindex(ICR)
10. EStatetopologicalparameter(TIE)
11. Maximalelectrotopologicalnegativevariation(MAXDN)
12. Maximalelectrotopologicalpositivevariation(MAXDP)
13. Molecularelectrotopologicalvariation(DELS)
14. WienerIndex(W)
15. MeanWienerIndex(WA)

ThefirstZagrebindex(weightedbyvertexdegrees)isgivenby
2
ZM1 = a a

(1)

wherearunsovertheAatomsofthemoleculeand a isthevertexdegreeofatoma.
ZM1V = a av
2

(2)

ZM 2 = b ( i j )b

(3)

(4)

where av isthevalencevertexdegreeofatoma.

wherebrunsoverallofthebondsinthemolecule.
ZM 2V = b iv vj

TheZagrebindices(ZM1,ZM1V,ZM2,andZM2V)aredescribedonpg509oftheHandbook
ofMoleculardescriptors(TodeschiniandConsonni2000).

TheBalabandistanceconnectivityindex(J)isgivenby
B
( i j )b 1/ 2
J=

(5)

C +1 b
where i and j arethevertexdistancedegreesoftwoadjacentatoms,andthesumrunsover
allthemolecularbondsb;Bisthenumberofbonds,andC(thecyclomaticnumber)isthe
numberofrings.Thevertexdistancedegree( i )isthesumofthedistancesofalltheother
atomstoagivenatom:
A

i = d ij

j =1

wheredijisthetopologicaldistancebetweenatomsiandj.

16

(6)

Thecyclomaticnumberisgivenby:

C = B A + 1

Asimilarindex,theJtindex,isdefinedasfollows:
B
1/ 2
Jt =
(t i t j )b
C +1 b
wheretiisadifferentlocalvertexinvariantgivenby

ti =

(7)

(8)

(9)

JandJtaredescribedonpg21oftheHandbookofMoleculardescriptors(Todeschiniand
Consonni2000).

Tocalculatethecentricindices,theverticeswithavertexdegreeofunityarestepwiseremoved
untilnomoreverticescanberemoved.TheBalabancentricindexiscalculatedasfollows:
R

BAC = n g
2

(10)

g =1

wherengisthenumberofatomswithavertexdegreeofunityremovedatstepgandRisthe
numberofremovalsteps.

TheLoppingcentricindexiscalculatedasfollows:
R n
ng
g
Lop = log

(11)
i =1 A
A
BACandLoparedescribedonpg42oftheHandbookofMoleculardescriptors(Todeschiniand
Consonni2000).

Theradialcentricinformationindex(ICR)iscalculatedasfollows:
G n
ng
g
ICR = log 2

(12)
A
g 1 A

wherengisthenumberofverticeshavingequalatomeccentricities( )inthegthclass,Gisthe
numberofequivalenceclasses,andAistheatomnumber.Theatomeccentricityisthe
maximumdistancefromtheithvertextotheothervertices:

i = max (d ij )
(13)
j

ICRisdescribedonpg44oftheHandbookofMoleculardescriptors(TodeschiniandConsonni
2000).

Voeckel(1994)definestheEStatetopologicalparameter(TIE)asfollows:
B B
(S i S j )b 1/ 2

(14)
TIE =

C + 1 b =1
InordertomatchthedescriptorusedinDragon(Talete2006)(andtobeabletocalculateTIEfor
compoundswithatomswithnegativeEStatevalues)theEStatetopologicalparameterisinstead
givenby:

17

B B
(1 + exp(S i ) exp(S j ) )b1 / 2

(15)
TIE =

C + 1 b =1
whereBisthenumberofbonds,Cisthecyclomaticnumber,SiistheEStateforatomi.TIEis
describedonpg165oftheHandbookofMoleculardescriptors(TodeschiniandConsonni2000).

Themaximalelectrotopologicalnegativevariation(MAXDN)isgivenby
MAXDN = max I i if I i < 0 i = 1,...A

(16)
i

where I i isthefieldeffectontheithatomduetotheperturbationofallotheratoms:
Ii I j
I i =

2
j (d ij + 1)

Similarlythemaximalelectrotopologicalpositivevariation(MAXDP)isgivenby
MAXDP = max I i if I i > 0 i = 1,...A

(18)

Themolecularelectrotopologicalvariation(DELS)isgivenby
DELS = I i

(19)

(17)

MAXDN,MAXDP,andDELSaredescribedinmoredetailbyGramatica(Gramaticaetal.
2000).

TheWienerindex(W)isgivenby
1 A A

(20)
W = d ij
2 i =1 i =1
wheredijisthetopologicaldistancebetweenatomsiandj.

ThemeanWienerindexisgivenby
2W
WA =

(21)
A( A 1)
WandWAaredescribedinmoredetailonpg497oftheHandbookofMoleculardescriptors
(TodeschiniandConsonni2000).

18

VI.MolecularFragments(234)

1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
29.
30.
31.
32.
33.
34.
35.
36.
37.
38.
39.
40.
41.
42.

43.
44.
45.
46.
47.
48.
49.
50.
51.
52.
53.
54.
55.
56.
57.
58.
59.
60.
61.
62.
63.
64.
65.
66.
67.
68.
69.
70.
71.
72.
73.
74.
75.
76.
77.
78.
79.
80.
81.
82.
83.
84.
85.
86.

ACAC
AN[attachedtoANinsamering]
ANH[attachedtoANinsamering]
C=C=O
C=[N+][O]
C=[N+]=(Aguiaraetal.)
N=S=O
N=[N+]=(Aguiaraetal.)
[N+]#N
A[N+][O]
N+[foursinglebonds]
CH2=C(CH3)C(=O)O
CH2=CHC(=O)O
N=C=S
SC(=S)S
SC(=S)O
SC(=O)S
SC(=O)O
OC(=S)O
C(=O)OC(=O)
NH[3memberedring]
N<[3memberedring]
NH2[attachedtoP]
NH[attachedtoP]
N<[attachedtoP]
Sn=O
Sn[oxygenattach]
Sn[aromaticattach]
Sn
Si[aromaticattach]
Si[oxygen,aromaticattach]
Si[oxygenattach]
Si
S(=O)(=O)[2nitrogenattach]
S(=O)(=O)[nitrogen,aromatic
attach]
S(=O)(=O)[aromaticattach]
S(=O)(=O)[olefinicattach]
S(=O)(=O)[nitrogen,aliphatic
attach]
S(=O)(=O)[aliphaticattach]
S(=O)[2nitrogenattach]
S(=O)[nitrogen,aromaticattach]
S(=O)[aromaticattach]

19

S(=O)olefinicattach]
S(=O)[nitrogen,aliphaticattach]
S(=O)[aliphaticattach]
OH[aromaticattach]
SH[aromaticattach]
N=O[aromaticattach]
ONO2
NO2[aromaticattach]
NO2[olefinicattach]
NO2[nitrogenattach]
NO2[aliphaticattach]
N=C=O[aromaticattach]
N=C=O[aliphaticattach]
COOH[aromaticattach]
OC(=O)O
C(=O)O[aromaticattach]
C(=O)SH[aromaticattach]
C(=O)S[aromaticattach]
C(=S)SH[aromaticattach]
C(=S)S[aromaticattach]
C(=S)OH[aromaticattach]
C(=S)O[aromaticattach]
C(=S)[nitrogen,aromaticattach]
C(=S)[aromaticattach]
CHO[aromaticattach]
COOH[aliphaticattach]
HC(=O)O
C(=O)O[nitrogenattach]
C(=O)O[cyclic]
C(=O)O[olefinicattach]
C(=O)O[aliphaticattach]
C(=O)SH[nitrogenattach]
C(=O)SH[aliphaticattach]
C(=O)S[nitrogenattach]
C(=O)S[aliphaticattach]
C(=S)SH[nitrogenattach]
C(=S)SH[aliphaticattach]
C(=S)OH[aliphaticattach]
C(=S)O[nitrogenattach]
C(=S)O[aliphaticattach]
C(=S)S[nitrogenattach]
C(=S)S[aliphaticattach]
C(=S)[2nitrogenattach]
C(=S)[nitrogen,aliphaticattach]

133. P=N
134. P=S
135. P(=O)
136. As(=O)
137. SH[aliphaticattach]
138. S[threememberedring]
139. S[sulfurattach]
140. S[arsenicattach]
141. S[phosphorusattach]
142. S[nitrogenattach]
143. S[2aromaticattach]
144. S[aromaticattach]
145. OH[sulfurattach]
146. OH[oxygenattach]
147. OH[arsenicattach]
148. OH[phosphorusattach]
149. OH[nitrogenattach]
150. OH[aliphaticattach]
151. O(epoxide)
152. O[2aromaticattach]
153. O[phosphorus,aromaticattach]
154. O[2phosphorusattach]
155. O[phosphorusattach]
156. O[arsenicattach]
157. O[nitrogenattach]
158. O[sulfurattach]
159. O[oxygenattach]
160. O[aromaticattach]
161. CH=[aromaticattach]
162. >C=[aromaticattach]
163. C#[aromaticattach]
164. CH3[aromaticattach]
165. CH2[aromaticattach]
166. CH<[aromaticattach]
167. >C<[aromaticattach]
168. CH3[aliphaticattach]
169. CH2[aliphaticattach]
170. CH<[aliphaticattach]
171. >C<[aliphaticattach]
172. =C=
173. =CH2[aliphaticattach]
174. =CH[aliphaticattach]
175. =C[aliphaticattach]
176. #CH[aliphaticattach]
177. #C[aliphaticattach]
178. NH2[aromaticattach]

87. C(=S)[aliphaticattach]
88. CF3[aromaticattach]
89. CCl3[aromaticattach]
90. C#N[aromaticattach]
91. CH=NOH
92. CH=NO
93. >C=NOH
94. >C=NO
95. C([H])=N[H][Nitrogenattach]
96. C([H])=N[Nitrogenattach]
97. >C=N[H][2Nitrogenattach]
98. >C=N[H][Nitrogenattach]
99. >C(=N)[2Nitrogenattach]
100. >C(=N)[Nitrogenattach]
101. CH=NH
102. >C=NH
103. CH2=N
104. CH=N
105. >C=N
106. NHN=O
107. >NN=O
108. N(=O)
109. N=NH
110. N=N
111. NH2[nitrogenattach]
112. NH[nitrogenattach]
113. N<[nitrogenattach]
114. CHO[nitrogenattach]
115. CHO[aliphaticattach]
116. C(=O)[halogenattach]
117. C(=O)[2aromaticattach]
118. C(=O)[nitrogen,aromaticattach]
119. C(=O)[aromaticattach]
120. C(=O)[2nitrogenattach]
121. C(=O)[nitrogen,aliphaticattach]
122. C(=O)[phosphorusattach]
123. C(=O)[olefinicattach]
124. C=O(ketone,aliphaticattach)
125. C=O(nonketone,aliphaticattach)
126. CCl3[aliphaticattach]
127. CF3[aliphaticattach]
128. C#N[aliphaticnitrogenattach]
129. C#N[aliphaticsulfurattach]
130. C#N[olefinicattach]
131. C#N[aliphaticattach]
132. P=NH

20

179. NH[aromaticattach]
180. N<[aromaticattach]
181. NH2[aliphaticattach]
182. NH[aliphaticattach]
183. N<[aliphaticattach]
184. Fusedaromaticcarbon
185. Fusedaromaticnitrogen
186. ACH
187. ANH
188. AC
189. AN
190. AN+
191. AO
192. AS
193. =O[other]
194. =S[other]
195. [O]
196. O[aliphaticattach]
197. S[aliphaticattach]
198. F[aromaticattach]
199. Br[aromaticattach]
200. Cl[aromaticattach]
201. I[aromaticattach]
202. Br[olefinicattach]
203. Cl[olefinicattach]
204. F[olefinicattach]
205. I[olefinicattach]
206. Halogen[Nitrogenattach]
207. Br[aliphaticattach]

208. Cl[aliphaticattach]
209. F[aliphaticattach]
210. I[aliphaticattach]
211. H[phosphorusattach]
212. H[nitrogenattach]
213. H[siliconattach]
214. H[carbonattach]
215. H[other]
216. Hg
217. Hg
218. Hg+
219. Hg
220. Pb
221. B
222. P[+3valence,allsinglebonds]
223. P[+3valence,allsinglebonds]
224. P[+3valence,allsinglebonds]
225. P[+5valence,onedoublebond]
226. P[+5valence,twodoublebonds]
227. P[+5valence,allsinglebonds]
228. P
229. As[+3valence,onedoublebond]
230. As[+3valence,allsinglebonds]
231. As[+5valence,onedoublebond]
232. As[+5valence,twodoublebonds]
233. As[+5valence,allsinglebonds]
234. As

21

Themolecularfragmentcounts(Martinetal.2008)representthenumberoftimesvarious

fragmentsappearinamolecule.ThefragmentsarewritteninaformatsimilartoSMILES
notation(DaylightChemicalInformationSystems2006).Thefragmentsweredesignedsothat
eachatominamoleculeisonlyassignedtoonefragment.Dashes()representsinglebonds,
Carats(<)representtwosinglebonds,equalsigns(=)representdoublebonds,andpoundsigns
(#)representtriplebonds.Thetermsinsidethebracketsprovideadditionalinformationsuchas
whatthefragmentisattachedto.Forexample,
O[phosphorus,aromaticattach]isthecountofoxygenatomsthatareattachedtoa
phosphorusatomandanaromaticatom.Thephosphorusatomandthearomaticatomarenot
consideredtobepartofthefragment.Inadditiontheterminsidethebracketscanindicate
whetherthefragmentispartofaring(forexample
S[threememberedring])orindicatethevalencestateofagivenelement(forexampleAs
[+3valence,onedoublebond]).Thefragmentsareassignedintheorderthattheyappear
above.Forexample1,2dichlorobenzenewouldhavethefollowingfragmentcounts:
Cl[aromaticattach]=2,AC=2,andACH=4.

22

VII.2DMolecularProperties(9)

1.
2.
3.
4.
5.
6.
7.
8.
9.

Numberofhydrogenbondacceptors(numHBa)
Numberofhydrogenbonddonors(numHBd)
Numberofweakhydrogenbonddonors(i.e.CHX,whereX=Cl,F)(numwHBd)
SumofEStateindicesforhydrogenbondacceptors(SHHBa)
SumofEStateindicesforhydrogenbonddonors(SHHBd)
SumofEStateindicesforweakhydrogenbonddonors(SHwHBd)
Molecularandgrouppolarityindex(Qs)
Molecularandgrouppolarityindex(Qv)
AverageofQsandQv(Qsv)

Thenumberofhydrogenbondacceptors(numHBa)isthetotalcountoffluorine,oxygen,
nonaromaticnitrogens,andaromaticnitrogenswithanEstatefragmentofSaaN(pyrrolyl
nitrogensarenotconsideredtobehydrogenbondacceptors).

Thenumberofhydrogenbonddonors(numHBd)isthetotalcountofhydrogensthatareattached
tooxygenornitrogenatoms.

Thenumberofweakhydrogenbonddonors(numwHBd)isthecountofcarbonatomsthathave
bothahydrogenatomandachlorineorfluorineatomattached.

ThesumofEStateindicesforhydrogenbondacceptors(SHHBa)isthesumoftheEstate
indicesforatomsthatareassignedtobehydrogenbondacceptors.

ThesumofEStateindicesforhydrogenbonddonors(SHHBd)isthesumofthehydrogenE
stateindicesforoxygensandnitrogens.

ThesumoftheEStateindicesforweakhydrogenbonddonors(SHwHBd)isthesumofthe
hydrogenEStatesforthecarbonatomsthathavebothahydrogenandachlorineorfluorine
attached.

TheQsmolecularandgrouppolarityindexisgivenby
A

Qs =

A 2 I ialkane
i=1

(1)
2
A

Ii
i=1
alkane
=Theintrinsicstatevalueofanatomconsideringallnonhydrogenatomshave
whereIi
beenreplacedbysp3carbonatoms(keepingthesameisoconnectivity).

TheQvmolecularandgrouppolarityindexisgivenby
A

Qv =

Ii

max

i=1

23

Ii

alkane

i=1

Ii
i=1
A

(2)

whereIimax=Theintrinsicstatevalueoftheatomwherethefollowingreplacementshavebeen
made:
(a) allterminalatoms(atomsbondedtooneothernonhydrogenatom)replacedby
F(I=8.000)
(b) alldivalentatoms(atomsbondedtotwoothernonhydrogenatoms)replacedby
O(I=3.500)
(c) alltrivalentatoms(atomsbondedtothreeothernonhydrogenatoms)replacedby
>N(I=2.000)
(d) allquaternaryatoms(atomsbondedtofourothernonhydrogenatoms)replacedby
>C<(I=1.250).

TheaverageofQsandQvisgivenby
A

Qsv =

Ii Ii
ave

i =1

alkane

i =1

Ii
i =1

(3)

where
A

Ii

i =1

ave

Ii

alkane

i =1

+ I imax
i =1

TheequationsforQs,Qv,andQsvweretakenfromdocumentationforMDLQSAR
(Elsevier_MDL2006).

24

(4)

VIII.InformationIndices(36)

A.ConnectivityBased(8)
1. Informationbondindex(ib)
2. Meaninformationcontentontheedgemagnitude(eim)
3. Informationcontent(ic)
4. MeaninformationcontentorShannonsentropy(si)
5. Totalinformationcontent(I)
6. Maximuminformationcontent(maxICormaxic)
7. StandardizedShannonInformationorstandardizedinformationcontent(ssi)
8. Brillouinredundancyindex(R)

Theinformationbondindexisgivenby
ib = B log 2 (B ) B g log 2 (B g )
GB

g =1

(1)

whereB=thenumberofbondsinthemolecule,Bg=thenumberofbondsoftypeginthe
molecule,andGB=allofthedifferentbondtypesinthemolecule.

Themeaninformationcontentontheedgemagnitude(eim)isbasedonthemagnitudeofedge
connectivitiesandisgivenby
1/ 2
B ( )
( i j )1/ 2
i j b
b

eim =
log 2

(2)
1
1

b=1

1/ 2
1
where isthefirstorderChiconnectivityindex(x1inSectionI), ( i j )b istheedge
connectivityofthebbond,andBisthenumberofbonds.

Theinformationcontent(ameasureofmolecularsymmetry)ofasystemhavingnelementsis
givenby
ic = n g log 2 (n g )
G

g =1

(3)

wherengisthenumberoftopologicallyequivalentatomsoftypegandGisthenumberof
topologicallydifferentatomtypes.Theinformationcontentisthesameasthezerothorder
kappashapeindexorKiersymmetryindex(Kier1987).Eachequivalencetypeisconstitutedby
allatomshavingthesamevalencetopologicalstate(Sv).Thevalencetopologicalstateisgiven
by
A

Svi = t ijv

(4)

(5)

i 1

where tijv isthevalencetopologicalstatematrixgivenby

t ijv = GM ijv (1/ nij )

25

wherenijisthenumberofatomsinthepathofmthorder. GM ijv isthegeometricmeanofthe

valencevertexdegreeoftheatomsinvolvedinthepathbetweenatomsiandjoflengthmandis
definedas:
nij v
GM = a

a =1
Themeaninformationcontentisdefinedasfollows:
v
ij

1/ nij

(6)

si = p g log 2 ( p g )

(7)

g =1

wherepg=theprobability(ng/n)ofselectingthegthtopologicalequivalenttype.Formolecules,
thetotalnumberofelementsinthesystem(n)isthesameasA(thenumberofnonhydrogen
atoms).

Thetotalinformationcontent(I)isobtainedbymultiplyingthemeaninformationcontentbythe
numberofelements:
I = n si
(8)

Themaximuminformationcontent(maxic)representstheinformationcontentneededto
characterizeallofthenalternatives:
maxic = n log 2 (n )
(9)

Thestandardizedinformationcontent(ssi)istheratiobetweenthetotalinformationcontentand
themaximuminformationcontent:
I

(10)
ssi =
maxic

Brillouinredundancyindex(R),ameasureoftheinformationredundancyofasystemisgivenby
(11)
R = 1 ssi

Theconnectivitybasedinformationindicesaredescribedinmoredetailonpages238240ofthe
HandbookofMolecularDescriptors(TodeschiniandConsonni2000).

TopologicallyBased(28)
E
1. Totalinformationcontentontheadjacencyequality( V I adj
oriadje)
E
2. Meaninformationcontentontheadjacencyequality( V I adj
oriadjem)
M
3. Totalinformationcontentontheadjacencymagnitude( V I adj
oriadjm)
M
4. Meaninformationcontentontheadjacencymagnitude( V I adj
oriadjmm)
E
5. Meaninformationcontentofthevertexdegreeequality( V I adj,deg
orivdem)
M
6. Meaninformationcontentofthevertexdegreemagnitude( V I adj,deg
orivdmm)
E
7. Totalinformationcontentontheedgeadjacencyequality( E I adj
orieadje)
E
8. Meaninformationcontentontheedgeadjacencyequality( E I adj
orieadjem)

26

M
9. Totalinformationcontentontheedgeadjacencymagnitude( E I adj
orieadjm)
M
10.Meaninformationcontentontheedgeadjacencymagnitude( E I adj
orieadjmm)

11.Totalinformationcontentonthedistanceequality( V I DE oride)
12.Meaninformationcontentonthedistanceequality( V I DE oridem)
13.Totalinformationcontentonthedistancemagnitude( V I DM oridm)
14.Meaninformationcontentonthedistancemagnitude( V I DM oridmm)
E
15.Meaninformationcontentonthedistancedegreeequality( V I D,deg
oriddem)

16.Meaninformationcontentonthedistancedegreemagnitude( V I DM,deg oriddmm)

17.Totalinformationcontentontheedgedistanceequality( E I DE oriede)
18.Meaninformationcontentontheedgedistanceequality( E I DE oriedem)
19.Edgewienerindex(We)
20.Totalinformationcontentontheedgedistancemagnitude( E I DM oriedm)
21.Meaninformationcontentontheedgedistancemagnitude( E I DM oriedmm)
22.Totalvertexcyclicity(tvc)
E
oricyce)
23.Totalinformationonthevertexcyclematrixequality( V I cyc
E
24.Meaninformationonthevertexcyclematrixequality( V I cyc
oricycem)
M
25.Totalinformationonthevertexcyclematrixmagnitude( V I cyc
oricycm)
M
26.Meaninformationonthevertexcyclematrixmagnitude( V I cyc
oricycmm)
27.Totaltopologicalindex(tti)
28.Totaltopologicalvalenceindex(ttvi)

Thetotalinformationcontentontheadjacencyequality(iadje)isgivenby
iadje = A 2 log 2 A 2 2B log 2 (2B ) A 2 2B log 2 A 2 2B
(12)

Themeaninformationcontentontheadjacencyequality(iadjem)isgivenby
2B
2B 2B
2B

(13)
iadjem = 2 log 2 2 1 2 log 2 1 2
A
A
A
A

whereA=thenumberofnonhydrogenatomsinmolecule(sameasabove)andB=thenumber
ofbondsinthemolecule(sameasabove).TheelementsoftheAdjacencyMatrix,aij,equal1if
theithatomandthejthatomarebondedtogetherandequal0ifnot.

Thetotalinformationcontentontheadjacencymagnitude(iadjm)isgivenby
iadjm = 2B log 2 (2B )
(14)

Themeaninformationcontentontheadjacencymagnitude(iadjmm)isgivenby
iadjmm = 1+ log 2 (B )
(15)

Themeaninformationcontentofthevertexdegreeequality(ivdem)isgivenby

( )

27

 gF
F
log 2

g 1 A
A
g
F isthenumberofverticeswithvertexdegreeequaltog.

Themeaninformationcontentofthevertexdegreemagnitude(ivdmm)isgivenby
G
g
g
ivdmm = g F
log 2

2B
2B
g 1
G

ivdem =

(16)

(17)

Thetotalinformationcontentontheedgeadjacencyequality(ieadje)isgivenby
ieadje = B 2 log 2 B 2 2N 2 log 2 (2N 2 ) B 2 2N 2 log 2 B 2 2N 2

Themeaninformationcontentontheedgeadjacencyequality(ieadjem)isgivenby
2N
2N 2N
2N
ieadjem = 22 log 2 22 1 22 log 2 1 22
B
B
B
B

nd
whereN2=thenumberof2 orderpathcountsinthemolecule.

Thetotalinformationcontentontheedgeadjacencymagnitude(ieadjm)isgivenby
ieadjm = 2N 2 log 2 (2N 2 )

( )

(18)

(19)

(20)

Themeaninformationcontentontheedgeadjacencymagnitude(ieadjmm)isgivenby
ieadjmm = 1 + log 2 ( N 2 )
(21)

Thetotalinformationcontentonthedistanceequality(ide)isgivenby
A( A 1)
A( A 1) G g
g
ide =
log 2

(22)
f log 2 f
2
2

g =1
where g f isthenumberofdistanceswithequalgvaluesinthetriangularDsubmatrix.DisanA
xAmatrixthatcontainsthegraphdistancesbetweenatoms.Thegraphdistancesarecalculated
as1/(the#ofbondsbetweenatoms)2.

Themeaninformationcontentonthedistanceequality(idem)isgivenby
G
2 g f
2 g f

idem =
log 2

(23)
g =1 A( A 1)
A( A 1)
Thetotalinformationcontentonthedistancemagnitude(idm)isgivenby

( )

idm = W log 2 (W ) g f g log 2 ( g )

(24)

Themeaninformationcontentonthedistancemagnitude(idmm)isgivenby
G
g
g
idmm = g f log 2

W
W
g =1

Themeaninformationcontentonthedistancedegreeequality(iddem)

(25)

28

 ng
log 2

(26)
g 1 A
A
wherengisthenumberofverticeshavingequalvertexdistancedegrees( )inthegthclass,Gis
thenumberofequivalenceclasses.

Themeaninformationcontentonthedistancedegreemagnitude(iddmm)isgivenby
G
g
g

iddmm = n g
log 2

(27)
2W
2
W
g 1

Thetotalinformationcontentontheedgedistanceequality(iede)isgivenby
B (B 1)
B (B 1)
g
g

(28)
iede =
log 2
f log 2 ( f )
2
2

Themeaninformationcontentontheedgedistanceequality(iedem)isgivenby
2 g f
2 g f

iedem =
log 2

(29)
B(B 1)
B(B 1)

Theedgewienerindex(We)isgivenby
A( A 1)
We = W

(30)
2

Thetotalinformationcontentontheedgedistancemagnitude(iedm)isgivenby
G

iddem =

ng

iedm = We log 2 (We ) g f g log 2 ( g )

(31)

Themeaninformationcontentontheedgedistancemagnitude(iedmm)isgivenby
g
g

iedmm = g f
log 2

We
We

Thetotalvertexcyclicity(tvc)isgivenby

(32)

A C+

tvc = cij
i =1 j =1

(33)

whereC+=thenumberofcyclesinamolecule(e.g.Naphthalenehas3cycles)andcij=1ifthe
ithatomispartofthejthcycleand0otherwise.Theelementscijcomprisethevertexcycle
matrixCV.

Thetotalinformationonthevertexcyclematrixequality(icyce)isgivenby
icyce = A C + log 2 A C + n1 log 2 (n1 ) n0 log 2 (n0 )
(34)

wheren0=thetotalnumberofcijelementsthatareequalto0andn1=thetotalnumberofcij
elementsthatareequalto1.

Themeaninformationonthevertexcyclematrixequality(icycem)isgivenby

29

icycem =

n1
n0
n
n
log 2 1 +
log 2 0 +
+
+
AC
AC AC
AC

Thetotalinformationonthevertexcyclematrixmagnitude(icycm)isgivenby
icycm = n1 log 2 (n1 )

Themeaninformationonthevertexcyclematrixmagnitude(icycmm)isgivenby
icycmm = log 2 (n1 )

Thetotaltopologicalindex(tti)isgivenby
A1 A

tti = t ii + t ij
i =1

i =1 j = i +1

(35)

(36)

(37)

(38)

where

(39)
t ij = GM ij (1/ nij )

whereGMijisthegeometricmeanofthevertexdegreeoftheatomsinvolvedinthepathijof
lengthm:
1/ nij

nij
GM ij = a
(40)

a =1
whereaisthevertexdegreeofatoma(definedinSectionII)andnij=thenumberofatomsin
thepathfromatomitoatomj.

Thetotaltopologicalvalenceindex(ttvi)isgivenby

A1

ttiv = t iiv +
i =1

v
ij

(41)

i =1 j = i +1

wheretheelementsofthevalencetopologicalstatematrixarecalculatedusingequations5and6.
Thetopologicallybasedinformationindicesaredescribedingreaterdetailonpages447457of
theHandbookofMolecularDescriptors(TodeschiniandConsonni2000).

30

IX.MolecularDistanceEdgeVector(19)

1.

Moleculardistanceedgebetweenallprimarycarbons(MDEC11)

2.

Moleculardistanceedgebetweenallprimaryandsecondarycarbons(MDEC12)

3.

Moleculardistanceedgebetweenallprimaryandtertiarycarbons(MDEC13)

4.

Moleculardistanceedgebetweenallprimaryandquaternarycarbons(MDEC14)

5.

Moleculardistanceedgebetweenallsecondarycarbons(MDEC22)

6.

Moleculardistanceedgebetweenallsecondaryandtertiarycarbons(MDEC23)

7.

Moleculardistanceedgebetweenallsecondaryandquaternarycarbons(MDEC24)

8.

Moleculardistanceedgebetweenalltertiarycarbons(MDEC33)

9.

Moleculardistanceedgebetweenalltertiaryandquaternarycarbons(MDEC34)

10.

Moleculardistanceedgebetweenallquaternarycarbons(MDEC44)

11.

Moleculardistanceedgebetweenallprimaryoxygens(MDEO11)

12.

Moleculardistanceedgebetweenallprimaryandsecondaryoxygens(MDEO12)

13.

Moleculardistanceedgebetweenallsecondaryoxygens(MDEO22)

14.

Moleculardistanceedgebetweenallprimarynitrogens(MDEN11)

15.

Moleculardistanceedgebetweenallprimaryandsecondarynitrogens(MDEN12)

16.

Moleculardistanceedgebetweenallprimaryandtertiarynitrogens(MDEN13)

17.

Moleculardistanceedgebetweenallsecondarynitrogens(MDEN22)

18.

Moleculardistanceedgebetweenallsecondaryandtertiarynitrogens(MDEN23)

19.

Moleculardistanceedgebetweenalltertiarynitrogens(MDEN33)

Thegeneralformulaforthemoleculedistanceedgevectordescriptorsisasfollows:

st =

nst
d st

(1)

where st isthemoleculardistanceedgevectorbetweenatomtypessandt,nstisthenumberof
possibleatompairsforafixedcombinationofsandt,and d st isgivenby
d st = s t (d i(s), j (t ) )

1/ ( 2n st )

(2)

where d i(s), j (t ) isthedistance(theshortestpathlength)betweenatomiwithtypessandatomj

withtypet.Thegeometricmeantakesintoaccountallthedistancesbetweencarbonatomsiand
joftypessandt.ThedescriptorsaredenotedasMDEXstwhereXistheelement,sisthefirst
atomtypeandtisthesecondatomtype.Theatomtypeordegree(primary,secondary,or
tertiary)isdeterminedfromthecountofnonhydrogenatomsthatareattachedtoagivenatom.

31

Themoleculardistanceedgevectorsaredescribedonpage116oftheHandbookofMolecular
Descriptors(TodeschiniandConsonni2000).

32

X.BurdenEigenvalueDescriptors(64)

1. Highesteigenvaluen.1ofBurdenmatrix/weightedbyatomicmasses(BEHm1)
2. Highesteigenvaluen.2ofBurdenmatrix/weightedbyatomicmasses(BEHm2)
3. Highesteigenvaluen.3ofBurdenmatrix/weightedbyatomicmasses(BEHm3)
4. Highesteigenvaluen.4ofBurdenmatrix/weightedbyatomicmasses(BEHm4)
5. Highesteigenvaluen.5ofBurdenmatrix/weightedbyatomicmasses(BEHm5)
6. Highesteigenvaluen.6ofBurdenmatrix/weightedbyatomicmasses(BEHm6)
7. Highesteigenvaluen.7ofBurdenmatrix/weightedbyatomicmasses(BEHm7)
8. Highesteigenvaluen.8ofBurdenmatrix/weightedbyatomicmasses(BEHm8)
9. Lowesteigenvaluen.1ofBurdenmatrix/weightedbyatomicmasses(BELm1)
10.Lowesteigenvaluen.2ofBurdenmatrix/weightedbyatomicmasses(BELm2)
11.Lowesteigenvaluen.3ofBurdenmatrix/weightedbyatomicmasses(BELm3)
12.Lowesteigenvaluen.4ofBurdenmatrix/weightedbyatomicmasses(BELm4)
13.Lowesteigenvaluen.5ofBurdenmatrix/weightedbyatomicmasses(BELm5)
14.Lowesteigenvaluen.6ofBurdenmatrix/weightedbyatomicmasses(BELm6)
15.Lowesteigenvaluen.7ofBurdenmatrix/weightedbyatomicmasses(BELm7)
16.Lowesteigenvaluen.8ofBurdenmatrix/weightedbyatomicmasses(BELm8)
17.Highesteigenvaluen.1ofBurdenmatrix/weightedbyatomicvanderWaalsvolumes
(BEHv1)
18.Highesteigenvaluen.2ofBurdenmatrix /weightedbyatomicvanderWaalsvolumes
(BEHv2)
19.Highesteigenvaluen.3ofBurdenmatrix /weightedbyatomicvanderWaalsvolumes
(BEHv3)
20.Highesteigenvaluen.4ofBurdenmatrix /weightedbyatomicvanderWaalsvolumes
(BEHv4)
21.Highesteigenvaluen.5ofBurdenmatrix /weightedbyatomicvanderWaalsvolumes
(BEHv5)
22.Highesteigenvaluen.6ofBurdenmatrix /weightedbyatomicvanderWaalsvolumes
(BEHv6)
23.Highest eigenvaluen.7ofBurdenmatrix / weightedbyatomicvanderWaals volumes
(BEHv7)

33

24.Highesteigenvaluen.8ofBurdenmatrix/weightedbyatomicvanderWaalsvolumes
(BEHv8)
25.Lowesteigenvaluen.1ofBurdenmatrix/weightedbyatomicvanderWaalsvolumes
(BELv1)
26.Lowesteigenvaluen.2ofBurdenmatrix/weightedbyatomicvanderWaalsvolumes
(BELv2)
27.Lowesteigenvaluen.3ofBurdenmatrix/weightedbyatomicvanderWaalsvolumes
(BELv3)
28.Lowesteigenvaluen.4ofBurdenmatrix/weightedbyatomicvanderWaalsvolumes
(BELv4)
29.Lowesteigenvaluen.5ofBurdenmatrix/weightedbyatomicvanderWaalsvolumes
(BELv5)
30.Lowesteigenvaluen.6ofBurdenmatrix/weightedbyatomicvanderWaalsvolumes
(BELv6)
31.Lowesteigenvaluen.7ofBurdenmatrix/weightedbyatomicvanderWaalsvolumes
(BELv7)
32.Lowesteigenvaluen.8ofBurdenmatrix/weightedbyatomicvanderWaalsvolumes
(BELv8)
33.Highesteigenvaluen.1ofBurdenmatrix/weightedbyatomicSanderson
electronegativities(BEHe1)
34.Highesteigenvaluen.2ofBurdenmatrix/weightedbyatomicSanderson
electronegativities(BEHe2)
35.Highesteigenvaluen.3ofBurdenmatrix/weightedbyatomicSanderson
electronegativities(BEHe3)
36.Highesteigenvaluen.4ofBurdenmatrix/weightedbyatomicSanderson
electronegativities(BEHe4)
37.Highesteigenvaluen.5ofBurdenmatrix /weightedbyatomicSanderson
electronegativities(BEHe5)
38.Highesteigenvaluen.6ofBurdenmatrix /weightedbyatomicSanderson
electronegativities(BEHe6)
39.Highesteigenvaluen.7ofBurdenmatrix /weightedbyatomicSanderson
electronegativities(BEHe7)
40.Highesteigenvaluen.8ofBurdenmatrix /weightedbyatomicSanderson
electronegativities(BEHe8)
41.Lowest eigenvaluen.1ofBurdenmatrix / weightedbyatomicSanderson
electronegativities(BELe1)
42.Lowest eigenvaluen.2ofBurdenmatrix / weightedbyatomicSanderson
electronegativities(BELe2)

34

43.Lowesteigenvaluen.3ofBurdenmatrix/weightedbyatomicSanderson

electronegativities(BELe3)

44.Lowesteigenvaluen.4ofBurdenmatrix/weightedbyatomicSanderson

electronegativities(BELe4)

45.Lowesteigenvaluen.5ofBurdenmatrix/weightedbyatomicSanderson

electronegativities(BELe5)

46.Lowesteigenvaluen.6ofBurdenmatrix/weightedbyatomicSanderson

electronegativities(BELe6)

47.Lowesteigenvaluen.7ofBurdenmatrix/weightedbyatomicSanderson

electronegativities(BELe7)

48.Lowesteigenvaluen.8ofBurdenmatrix/weightedbyatomicSanderson

electronegativities(BELe8)

49.Highesteigenvaluen.1ofBurdenmatrix/weightedbyatomicpolarizabilities(BEHp1)
50.Highesteigenvaluen.2ofBurdenmatrix/weightedbyatomicpolarizabilities(BEHp2)
51.Highesteigenvaluen.3ofBurdenmatrix/weightedbyatomicpolarizabilities(BEHp3)
52.Highesteigenvaluen.4ofBurdenmatrix/weightedbyatomicpolarizabilities(BEHp4)
53.Highesteigenvaluen.5ofBurdenmatrix/weightedbyatomicpolarizabilities(BEHp5)
54.Highesteigenvaluen.6ofBurdenmatrix/weightedbyatomicpolarizabilities(BEHp6)
55.Highesteigenvaluen.7ofBurdenmatrix/weightedbyatomicpolarizabilities(BEHp7)
56.Highesteigenvaluen.8ofBurdenmatrix/weightedbyatomicpolarizabilities(BEHp8)
57.Lowesteigenvaluen.1ofBurdenmatrix/weightedbyatomicpolarizabilities(BELp1)
58.Lowesteigenvaluen.2ofBurdenmatrix/weightedbyatomicpolarizabilities(BELp2)
59.Lowesteigenvaluen.3ofBurdenmatrix/weightedbyatomicpolarizabilities(BELp3)
60.Lowesteigenvaluen.4ofBurdenmatrix/weightedbyatomicpolarizabilities(BELp4)
61.Lowesteigenvaluen.5ofBurdenmatrix /weightedbyatomicpolarizabilities(BELp5)
62.Lowesteigenvaluen.6ofBurdenmatrix /weightedbyatomicpolarizabilities(BELp6)
63.Lowesteigenvaluen.7ofBurdenmatrix /weightedbyatomicpolarizabilities(BELp7)
64.Lowesteigenvaluen.8ofBurdenmatrix /weightedbyatomicpolarizabilities(BELp8)

TheBurdeneigenvaluedescriptorsaredetermined bysolvingthefollowinggeneraleigenvalue
equation:
B V = V e

whereBisarealconnectivitymatrixtobedefined,Visamatrixofeigenvectors,andeisa
diagonalmatrixofeigenvalues.TherulesdefiningBareasfollows:
a. Hydrogenatomsareincluded.

35

(1)

b. ThediagonalelementsofB,Bii,areeithergivenbythecarbonnormalizedatomicmass,
vanderWaalsvolume,Sandersonelectronegativity,andpolarizabilityofatomi.
c. TheelementofBconnectingatomsiandj,Bij,isequaltothesquarerootofthebond
orderbetweenatomsiandj.
d. AllotherelementsofB(correspondingnonbondedatompairs)aresetto0.001.

Thecarbonnormalizedweightsusedinthesoftwareasfollows:

Symbol Mass VdWVolume Electronegativity Polarizability

C
1.000
1.000
1.000
1.000
H
0.084
0.299
0.942
0.381
N
1.167
0.695
1.160
0.625
O
1.332
0.512
1.327
0.455
P
2.579
1.181
0.916
2.063
S
2.670
1.088
1.076
1.648
F
1.582
0.410
1.455
0.318
Cl
2.952
1.000
1.265
1.239
Br
6.653
1.384
1.171
1.733
I
10.566
1.728
1.011
3.040
Si
2.339
1.424
0.778
3.057
As
6.238
1.181
1.025
2.449
Sn
9.884
2.041
0.836
4.375
Hg
16.702
0.695
0.800
3.239
Pb
17.252
1.538
0.833
3.864

Thelowesteigenvaluesaretheabsolutevaluesofthenegativeeigenvalues.Thehighest
eigenvaluesaretheeightlargestpositiveeigenvalues.Aroutineforsolvingforeigenvaluesis
foundintheJamaJavapackage(National_Institute_of_Standards_and_Technology2005).The
Burdeneigenvaluesdescriptorsaredescribedonpages132133oftheHandbookofMolecular
Descriptors(TodeschiniandConsonni2000).

36

XI.WalkandPathCounts(34)

1. Molecularwalkcountoforder01(MWC01)
2. Molecularwalkcountoforder02(MWC02)
3. Molecularwalkcountoforder03(MWC03)
4. Molecularwalkcountoforder04(MWC04)
5. Molecularwalkcountoforder05(MWC05)
6. Molecularwalkcountoforder06(MWC06)
7. Molecularwalkcountoforder07(MWC07)
8. Molecularwalkcountoforder08(MWC08)
9. Molecularwalkcountoforder09(MWC09)
10.Molecularwalkcountoforder10(MWC10)
11.Totalwalkcount(TWC)
12.Selfreturningwalkcountoforder01(SRW01)
13.Selfreturningwalkcountoforder02(SRW02)
14.Selfreturningwalkcountoforder03(SRW03)
15.Selfreturningwalkcountoforder04(SRW04)
16.Selfreturningwalkcountoforder05(SRW05)
17.Selfreturningwalkcountoforder06(SRW06)
18.Selfreturningwalkcountoforder07(SRW07)
19.Selfreturningwalkcountoforder08(SRW08)
20.Selfreturningwalkcountoforder09(SRW09)
21.Selfreturningwalkcountoforder10(SRW10)
22.Molecularpathcountoforder01(MPC01)
23.Molecularpathcountoforder02(MPC02)
24.Molecularpathcountoforder03(MPC03)
25.Molecularpathcountoforder04(MPC04)
26.Molecularpathcountoforder05(MPC05)
27.Molecularpathcountoforder06(MPC06)
28.Molecularpathcountoforder07(MPC07)
29.Molecularpathcountoforder08(MPC08)
30.Molecularpathcountoforder09(MPC09)
31.Molecularpathcountoforder10(MPC10)
32.Totalpathcount(TPC)
33.Molecularmultiplepathcountoforder01(piPC01)
34.Molecularmultiplepathcountoforder02(piPC02)
35.Molecularmultiplepathcountoforder03(piPC03)
36.Molecularmultiplepathcountoforder04(piPC04)
37.Molecularmultiplepathcountoforder05(piPC05)
38.Molecularmultiplepathcountoforder06(piPC06)
39.Molecularmultiplepathcountoforder07(piPC07)
40.Molecularmultiplepathcountoforder08(piPC08)
41.Molecularmultiplepathcountoforder09(piPC09)
42.Molecularmultiplepathcountoforder10(piPC10)
43.ConventionalbondorderIDnumber(piID)
44.RandicIDnumber(CID)
37

45.AverageRandicIDnumber(CID2)
46.BalabanIDnumber(BID)

Themolecularwalkcountofkthorder(MWCk)isthetotalnumberofwalksofthekthlengthin
thehydrogensuppressedmoleculargraphgivenby
1 A A
MWCk = aij(k )

(1)
2 i =1 j =1
where aij(k ) aretheelementsofAk(thekthpoweroftheadjacencymatrixA)andAisthenumber
ofatoms.TomatchDragon(Talete2006)thefollowingformulawasusedifkisgreaterthan
one:
A A

MWCk = ln aij(k ) + 1
(2)

i =1 j =1

Themolecularwalkcountdescriptorsaredescribedonpage481oftheHandbookofMolecular
Descriptors(TodeschiniandConsonni2000).

Thetotalwalkcount(TWC)isgivenby
A 1

A1

k =0

k =1

TWC = MWCk = A + MWCk

(3)

(4)

TomatchDragonthefollowingformulamustbeused:
10

TWC = A + MWCk

k =1

Theselfreturningwalkcountofkthorder(SRWk)isthetotalnumberofselfreturningwalksof
lengthkinthegraphandcalculatedasfollows:
(5)
SRWk=tr(Ak)

k
wheretristhetraceoperator(sumofthediagonalelements)andA isthekthpowerofthe
adjacencymatrix.Theselfreturningwalkcountdescriptorsaredescribedonpage384ofthe
HandbookofMolecularDescriptors(TodeschiniandConsonni2000).

Themolecularpathcounts(MPCk)aresimplythenumberofuniquepathsoflengthk.The
molecularpathcountdescriptorsaredescribedonpage345oftheHandbookofMolecular
Descriptors(TodeschiniandConsonni2000).

Thetotalpathcount(TPC)isobtainedbysummingallthemolecularpathcounts:
L

i =0

k =1

TPC = MPCk = A + MPCk

(6)

whereListhemaximumpathlength.InordertomatchDragonthetotalpathcountisinstead
givenby
L

TPC = A + ln(1+ MPCk)

k =1

Themolecularmultiplepathcounts(piPCk)aredefinedaspathcountsweightedbythebond
order:

38

(7)

piPCk = k p wij

(8)

ij

where k pij denotesapathoflengthkfromvertexitovertexjandwijisthepathweightgivenby

theproductofthebondordersinthepath:
k

wij = b*

(9)

b =1

Itshouldbenotedthataromaticbondsareassignedabondorderof1.5.Inordertomatch
Dragon,againasimilarlogarithmictransformationisusedtocalculatepiPCk:
piPCk = ln 1 + k p wij

ij

(10)

TheconventionalbondorderIDnumber(piID)iscalculatedasthesumofthemolecularmultiple
pathcounts:
L

k =0

k =1

piID = piPCk = A + piPCk

(11)

TheRandicIDnumberisalsodefinedasaweightedmolecularpathcount:
CID = A + k p wij

(12)

ij

whereAisthenumberofatoms, k pij denotesapathoflengthkfromvertexitovertexjandwijis

thepathweightgivenby
1/ 2

wij = ( b(1) b(2) )

m

b =1

(13)

where b(1) and b(2) arethevertexdegreeofthetwoatomsincidenttothebthedgeandbruns

overallofthemedgesofthepath.

TheaverageRandicIDnumberisgivenby
(14)
CID2 = CID / A

TheBalabanIDnumber(BID)iscalculatedusingthesameformulaasRandicIDnumber(CID)
exceptthepathweightisgivenby

= (

1/ 2

wij

b =1

b(1)

b(2)

(15)

where b(1) and b(2) arethevertexdistancedegreesofthetwoatomsincidenttothebthedgeand

brunsoverallofthemedgesofthepath.

CIDandBIDaredescribedonpages227and229,respectivelyoftheHandbookofMolecular
Descriptors(TodeschiniandConsonni2000).

39

XII.2DAutocorrelationDescriptors

1. BrotoMoreauautocorrelationofatopologicalstructurelag1/weightedbyatomic
masses(ATS1m)
2. BrotoMoreauautocorrelationofatopologicalstructurelag2/weightedbyatomic
masses(ATS2m)
3. BrotoMoreauautocorrelationofatopologicalstructurelag3/weightedbyatomic
masses(ATS3m)
4. BrotoMoreauautocorrelationofatopologicalstructurelag4/weightedbyatomic
masses(ATS4m)
5. BrotoMoreauautocorrelationofatopologicalstructurelag5/weightedbyatomic
masses(ATS5m)
6. BrotoMoreauautocorrelationofatopologicalstructurelag6/weightedbyatomic
masses(ATS6m)
7. BrotoMoreauautocorrelationofatopologicalstructurelag7/weightedbyatomic
masses(ATS7m)
8. BrotoMoreauautocorrelationofatopologicalstructurelag8/weightedbyatomic
masses(ATS8m)
9. BrotoMoreauautocorrelationofatopologicalstructurelag1/weightedbyatomicvan
derWaalsvolumes(ATS1v)
10.BrotoMoreauautocorrelationofatopologicalstructurelag2/weightedbyatomicvan
derWaalsvolumes(ATS2v)
11.BrotoMoreauautocorrelationofatopologicalstructurelag3/weightedbyatomicvan
derWaalsvolumes(ATS3v)
12.BrotoMoreauautocorrelationofatopologicalstructurelag4/weightedbyatomicvan
derWaalsvolumes(ATS4v)
13.BrotoMoreauautocorrelationofatopologicalstructurelag5/weightedbyatomicvan
derWaalsvolumes(ATS5v)
14.BrotoMoreauautocorrelationofatopologicalstructurelag6/weightedbyatomicvan
derWaalsvolumes(ATS6v)
15.BrotoMoreauautocorrelationofatopologicalstructurelag7/weightedbyatomicvan
derWaalsvolumes(ATS7v)
16.BrotoMoreauautocorrelationofatopologicalstructurelag8/weightedbyatomicvan
derWaalsvolumes(ATS8v)
17.BrotoMoreauautocorrelationofatopologicalstructurelag1/weightedbyatomic
Sandersonelectronegativities(ATS1e)
18.BrotoMoreauautocorrelationofatopologicalstructurelag2/weightedbyatomic
Sandersonelectronegativities(ATS2e)
19.BrotoMoreauautocorrelationofatopologicalstructurelag3/weightedbyatomic
Sandersonelectronegativities(ATS3e)
20.BrotoMoreauautocorrelationofatopologicalstructurelag4/weightedbyatomic
Sandersonelectronegativities(ATS4e)
21.BrotoMoreauautocorrelationofatopologicalstructurelag5/weightedbyatomic
Sandersonelectronegativities(ATS5e)
22.BrotoMoreauautocorrelationofatopologicalstructurelag6/weightedbyatomic
Sandersonelectronegativities(ATS6e)
40

23.BrotoMoreauautocorrelationofatopologicalstructurelag7/weightedbyatomic
Sandersonelectronegativities(ATS7e)
24.BrotoMoreauautocorrelationofatopologicalstructurelag8/weightedbyatomic
Sandersonelectronegativities(ATS8e)
25.BrotoMoreauautocorrelationofatopologicalstructurelag1/weightedbyatomic
polarizabilities(ATS1p)
26.BrotoMoreauautocorrelationofatopologicalstructurelag2/weightedbyatomic
polarizabilities(ATS2p)
27.BrotoMoreauautocorrelationofatopologicalstructurelag3/weightedbyatomic
polarizabilities(ATS3p)
28.BrotoMoreauautocorrelationofatopologicalstructurelag4/weightedbyatomic
polarizabilities(ATS4p)
29.BrotoMoreauautocorrelationofatopologicalstructurelag5/weightedbyatomic
polarizabilities(ATS5p)
30.BrotoMoreauautocorrelationofatopologicalstructurelag6/weightedbyatomic
polarizabilities(ATS6p)
31.BrotoMoreauautocorrelationofatopologicalstructurelag7/weightedbyatomic
polarizabilities(ATS7p)
32.BrotoMoreauautocorrelationofatopologicalstructurelag8/weightedbyatomic
polarizabilities(ATS8p)
33.Moranautocorrelationlag1/weightedbyatomicmasses(MATS1m)
34.Moranautocorrelationlag2/weightedbyatomicmasses(MATS2m)
35.Moranautocorrelationlag3/weightedbyatomicmasses(MATS3m)
36.Moranautocorrelationlag4/weightedbyatomicmasses(MATS4m)
37.Moranautocorrelationlag5/weightedbyatomicmasses(MATS5m)
38.Moranautocorrelationlag6/weightedbyatomicmasses(MATS6m)
39.Moranautocorrelationlag7/weightedbyatomicmasses(MATS7m)
40.Moranautocorrelationlag8/weightedbyatomicmasses(MATS8m)
41.Moranautocorrelationlag1/weightedbyatomicvanderWaalsvolumes(MATS1v)
42.Moranautocorrelationlag2/weightedbyatomicvanderWaalsvolumes(MATS2v)
43.Moranautocorrelationlag3/weightedbyatomicvanderWaalsvolumes(MATS3v)
44.Moranautocorrelationlag4/weightedbyatomicvanderWaalsvolumes(MATS4v)
45.Moranautocorrelationlag5/weightedbyatomicvanderWaalsvolumes(MATS5v)
46.Moranautocorrelationlag6/weightedbyatomicvanderWaalsvolumes(MATS6v)
47.Moranautocorrelationlag7/weightedbyatomicvanderWaalsvolumes(MATS7v)
48.Moranautocorrelationlag8/weightedbyatomicvanderWaalsvolumes(MATS8v)
49.Moranautocorrelationlag1/weightedbyatomicSandersonelectronegativities
(MATS1e)
50.Moranautocorrelationlag2/weightedbyatomicSandersonelectronegativities
(MATS2e)
51.Moranautocorrelationlag3/weightedbyatomicSandersonelectronegativities
(MATS3e)
52.Moranautocorrelationlag4/weightedbyatomicSandersonelectronegativities
(MATS4e)
53.Moranautocorrelationlag5/weightedbyatomicSandersonelectronegativities
(MATS5e)

41

54.Moranautocorrelationlag6/weightedbyatomicSandersonelectronegativities
(MATS6e)
55.Moranautocorrelationlag7/weightedbyatomicSandersonelectronegativities
(MATS7e)
56.Moranautocorrelationlag8/weightedbyatomicSandersonelectronegativities
(MATS8e)
57.Moranautocorrelationlag1/weightedbyatomicpolarizabilities(MATS1p)
58.Moranautocorrelationlag2/weightedbyatomicpolarizabilities(MATS2p)
59.Moranautocorrelationlag3/weightedbyatomicpolarizabilities(MATS3p)
60.Moranautocorrelationlag4/weightedbyatomicpolarizabilities(MATS4p)
61.Moranautocorrelationlag5/weightedbyatomicpolarizabilities(MATS5p)
62.Moranautocorrelationlag6/weightedbyatomicpolarizabilities(MATS6p)
63.Moranautocorrelationlag7/weightedbyatomicpolarizabilities(MATS7p)
64.Moranautocorrelationlag8/weightedbyatomicpolarizabilities(MATS8p)
65.Gearyautocorrelationlag1/weightedbyatomicmasses(GATS1m)
66.Gearyautocorrelationlag2/weightedbyatomicmasses(GATS2m)
67.Gearyautocorrelationlag3/weightedbyatomicmasses(GATS3m)
68.Gearyautocorrelationlag4/weightedbyatomicmasses(GATS4m)
69.Gearyautocorrelationlag5/weightedbyatomicmasses(GATS5m)
70.Gearyautocorrelationlag6/weightedbyatomicmasses(GATS6m)
71.Gearyautocorrelationlag7/weightedbyatomicmasses(GATS7m)
72.Gearyautocorrelationlag8/weightedbyatomicmasses(GATS8m)
73.Gearyautocorrelationlag1/weightedbyatomicvanderWaalsvolumes(GATS1v)
74.Gearyautocorrelationlag2/weightedbyatomicvanderWaalsvolumes(GATS2v)
75.Gearyautocorrelationlag3/weightedbyatomicvanderWaalsvolumes(GATS3v)
76.Gearyautocorrelationlag4/weightedbyatomicvanderWaalsvolumes(GATS4v)
77.Gearyautocorrelationlag5/weightedbyatomicvanderWaalsvolumes(GATS5v)
78.Gearyautocorrelationlag6/weightedbyatomicvanderWaalsvolumes(GATS6v)
79.Gearyautocorrelationlag7/weightedbyatomicvanderWaalsvolumes(GATS7v)
80.Gearyautocorrelationlag8/weightedbyatomicvanderWaalsvolumes(GATS8v)
81.Gearyautocorrelationlag1/weightedbyatomicSandersonelectronegativities
(GATS1e)
82.Gearyautocorrelationlag2/weightedbyatomicSandersonelectronegativities
(GATS2e)
83.Gearyautocorrelationlag3/weightedbyatomicSandersonelectronegativities
(GATS3e)
84.Gearyautocorrelationlag4/weightedbyatomicSandersonelectronegativities
(GATS4e)
85.Gearyautocorrelationlag5/weightedbyatomicSandersonelectronegativities
(GATS5e)
86.Gearyautocorrelationlag6/weightedbyatomicSandersonelectronegativities
(GATS6e)
87.Gearyautocorrelationlag7/weightedbyatomicSandersonelectronegativities
(GATS7e)
88.Gearyautocorrelationlag8/weightedbyatomicSandersonelectronegativities
(GATS8e)

42

89.Gearyautocorrelationlag1/weightedbyatomicpolarizabilities(GATS1p)
90.Gearyautocorrelationlag2/weightedbyatomicpolarizabilities(GATS2p)
91.Gearyautocorrelationlag3/weightedbyatomicpolarizabilities(GATS3p)
92.Gearyautocorrelationlag4/weightedbyatomicpolarizabilities(GATS4p)
93.Gearyautocorrelationlag5/weightedbyatomicpolarizabilities(GATS5p)
94.Gearyautocorrelationlag6/weightedbyatomicpolarizabilities(GATS6p)
95.Gearyautocorrelationlag7/weightedbyatomicpolarizabilities(GATS7p)
96.Gearyautocorrelationlag8/weightedbyatomicpolarizabilities(GATS8p)

TheBrotoMoreauautocorrelationdescriptors(ATSdw)aregivenby
A

ATSdw = ij wi w j

(1)

i =1 j =1

wheredistheconsideredtopologicaldistance(i.e.thelagintheautocorrelationterms), ij isthe
Kroneckerdeltafunction( ij =1ifdij=d,zerootherwise),andwiandwjaretheweights
(normalizedatomicproperties)foratomsiandjrespectively.Thenormalizedatomicmass,van
derWaalsvolume,electronegativity,orpolarizabilitycanbeusedfortheweights.Tomatch
Dragon(Talete2006),theBrotoMoreauautocorrelationdescriptorsarecalculatedinthe
softwareasfollows:
A A

ATSdw = ln1 + ij wi w j

(2)
i =1 j =1

TheMoranautocorrelationdescriptors(MATSdw)aregivenby
1 A A
ij (wi w ) (w j w )
i 1 j =1
MATSdw =

(3)
1 A
2
(wi w )
A i =1
where w istheaveragevalueofthepropertyforthemoleculeand
isthenumberofvertexpairsatdistanceequaltod.

43

TheGearyautocorrelationdescriptorsaregivenby
2
1 A A
ij (wi w j )
2 i1 j=1
GATSdw =

(4)
1 A
2
(wi w )
A 1 i=1

ThecarbonnormalizedweightsaregiveninSectionX(Burdeneigenvaluedescriptors).

The2Dautocorrelationdescriptorsaredescribedonpage1719oftheHandbookofMolecular
Descriptors(TodeschiniandConsonni2000).

44

XIII.Molecularproperties(7)

1.
2.
3.
4.
5.
6.
7.

GhoseCrippenoctanolwatercoefficient(ALOGP)
GhoseCrippenoctanolwatercoefficientsquared(ALOGP2)
GhoseCrippenmolarrefractivity(AMR)
Wangoctanolwaterpartitioncoefficient(XLOGP)
Wangoctanolwaterpartitioncoefficientsquared(XLOGP2)
Hydrophilicindex(Hy)
Unsaturationindex(Ui)

TheGhoseCrippenoctanolwatercoefficient(ALOGP)isagroupcontributionmodelforthe
octanolwaterpartitioncoefficient.ALOGPisdefinedasfollows:
(1)

ALOGP = k a k N k
whereakisthegroupcontributioncoefficientforthekthfragmenttypeandNkisthenumberof
occurrencesforthekthfragmenttype.TheALOGPdescriptorisdescribedingreaterdetailon
page275oftheHandbookofMolecularDescriptors(TodeschiniandConsonni2000)andby
Ghoseandcoworkers(Ghoseetal.1998).

ALOGP2issimplythesquareofALOGP:
(2)
ALOGP2 = ALOGP 2

TheGhoseCrippenmolarrefractivity(AMR)iscalculatedusingasimilargroupcontribution
approach:
AMR = k a kMR N kMR
(3)

where akMR isthemolarrefractivitygroupcontributioncoefficientforthekthmolarfragment

typeand N kMR isthenumberofoccurrencesforthekthmolarrefractivityfragmenttype.The
AMRdescriptorisdescribedinmoredetailbyViswanadhanandcoworkers(Viswanadhanetal.
1989).

TheWangoctanolwaterpartitioncoefficient(XLOGP)isalsocalculatedusingagroup
contributionmodel:
XLOGP = ai Ai + b j B j
(4)

whereAiistheoccurrenceoftheithatomtypeandBjistheoccurrenceofthejthcorrection
factor,aiisthecontributionoftheithatomtypeandbjisthecontributionofthejthcorrection
factor.TheXLOGPdescriptorisdescribedinmoredetailbyWangandcoworkers(Wangetal.
2000).

AgainXLOGP2issimplythesquareofXLOGP:
XLOGP 2 = XLOGP 2
(5)

Thehydrophilicityfactorisgivenby

45

N Hy
1
1
log 2 +
A
A2
A
Hy =

(6)
log 2 (1 + A)
whereNHyisthenumberofhydrophilicgroups(orthetotalnumberofhydrogensattachedto
oxygen,sulfur,ornitrogenatoms),NCisthenumberofcarbonatoms,andAisthenumberof
nonhydrogenatoms.Thehydrophilicityindexisdescribedinmoredetailonpage225ofthe
HandbookofMolecularDescriptors(TodeschiniandConsonni2000).

Theunsaturationindex(UI)isdefinedas
UI = log 2 (1 + nDB + nTB + nAB )
(7)

wherenDB=thenumberofdoublebonds,nTB=numberoftriplebonds,andnAB=numberof
aromaticbonds.TheunsaturationindexisdescribedintheusermanualforDragon(Talete
2006).

(1 + N )log (1 + N ) + N
Hy

Hy

46

XIV.References

Aguiara,P.F.d.,Bourguignon,B.,Khotsa,M.S.,Massarta,D.L.,andPhanThanLuub,R.
1995.Doptimaldesigns.ChemometricsandIntelligentLaboratorySystems30:199210.
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Martin, T.M.,Harten,P.,Venkatapathy,R.,Das,S.,andYoung,D.M.2008.AHierarchical
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47