Atom-centred fragments

Atom-centred fragments are those defined by Ghose and Crippen [V.N. Viswanadhan, A.K. Ghose, G.R. Revankar, R.K. Robins, J.Chem.Inf.Comput.Sci. 1989, 29, 163-172; Ghose et al, J.Phys.Chem. A, Vol. 102, No. 21, 1998]. Each atom type is an atom in the molecule described by its neighbouring atoms. Hydrogen and halogen atoms are classified by the hybridisation and oxidation state of the carbon atom to which they are bonded; for hydrogens, heteroatoms attached to a carbon atom in ?-position are further considered. Carbon atoms are classified by their hybridisation state and depending on whether their neighbours are carbon or heteroatoms.

 

Atom-centred fragments

ID

Symbol

Description

Hydrophobicity

MR

1

C-001

CH3R / CH4

-1.5603

2.9680

2

C-002

CH2R2

-1.0120

2.9116

3

C-003

CHR3

-0.6681

2.8028

4

C-004

CR4

-0.3698

2.6205

5

C-005

CH3X

-1.7880

3.0150

6

C-006

CH2RX

-1.2486

2.9244

7

C-007

CH2X2

-1.0305

2.6329

8

C-008

CHR2X

-0.6805

2.5040

9

C-009

CHRX2

-0.3858

2.3770

10

C-010

CHX3

0.7555

2.5590

11

C-011

CR3X

-0.2849

2.3030

12

C-012

CR2X2

0.0200

2.3006

13

C-013

CRX3

0.7894

2.9627

14

C-014

CX4

1.6422

2.3038

15

C-015

=CH2

-0.7866

3.2001

16

C-016

=CHR

-0.3962

4.2654

17

C-017

=CR2

0.0383

3.9392

18

C-018

=CHX

-0.8051

3.6005

19

C-019

=CRX

-0.2129

4.4870

20

C-020

=CX2

0.2432

3.2001

21

C-021

#CH

0.4697

3.4825

22

C-022

#CR / R=C=R

0.2952

4.2817

23

C-023

#CX

-

3.9556

24

C-024

R--CH--R

-0.3251

3.4491

25

C-025

R--CR--R

0.1492

3.8821

26

C-026

R--CX--R

0.1539

3.7593

27

C-027

R--CH--X

0.0005

2.5009

28

C-028

R--CR--X

0.2361

2.5000

29

C-029

R--CX--X

0.3514

3.0627

30

C-030

X--CH--X

0.1814

2.5009

31

C-031

X--CR--X

0.0901

-

32

C-032

X--CX--X

0.5142

2.6632

33

C-033

R--CH..X

-0.3723

3.4671

34

C-034

R--CR..X

0.2813

3.6842

35

C-035

R--CX..X

0.1191

2.9372

36

C-036

Al-CH=X

-0.1320

4.0190

37

C-037

Ar-CH=X

-0.0244

4.7770

38

C-038

Al-C(=X)-Al

-0.2405

3.9031

39

C-039

Ar-C(=X)-R

-0.0909

3.9964

40

C-040

R-C(=X)-X / R-C#X / X=C=X

-0.1002

3.4986

41

C-041

X-C(=X)-X

0.4182

3.4997

42

C-042

X--CH..X

-0.2147

2.7784

42

C-043

X--CR..X

-0.0009

2.6267

44

C-044

X--CX..X

0.1388

2.5000

45

H-046

Ha attached to C0(sp3) no X attached to next C

0.7341

0.8447

46

H-047

Ha attached to C1(sp3) / C0(sp2)

0.6301

0.8939

47

H-048

Ha attached to C2(sp3) / C1(sp2) / C0(sp)

0.5180

0.8005

48

H-049

Ha attached to C3(sp3) / C2(sp2) / C3(sp2) / C3(sp)

-0.0371

0.8320

49

H-050

H attached to heteroatom

-0.1036

0.8000

50

H-051

H attached to alpha-Cb

0.5234

0.8188

51

H-052

Ha attached to C0(sp3) with 1X attached to next C

0.6666

0.9215

52

H-053

Ha attached to C0(sp3) with 2X attached to next C

0.5372

0.9769

53

H-054

Ha attached to C0(sp3) with 3X attached to next C

0.6338

0.7701

54

H-055

Ha attached to C0(sp3) with 4X attached to next C

0.3620

-

55

O-056

alcohol

-0.3567

1.7646

56

O-057

phenol / enol / carboxyl OH

-0.0127

1.4778

57

O-058

=O

-0.0233

1.4429

58

O-059

Al-O-Al

-0.1541

1.6191

59

O-060

Al-O-Ar / Ar-O-Ar / R..O..R / R-O-C=X

0.0324

1.3502

60

O-061

O-- c

1.0520

1.9450

61

O-062

O- (negatively charged)

-0.7941

-

62

O-063

R-O-O-R

0.4165

-

63

Se-064

Any-Se-Any

0.6601

-

64

Se-065

=Se

-

-

65

N-066

Al-NH2

-0.5427

2.6221

66

N-067

Al2-NH

-0.3168

2.5000

67

N-068

Al3-N

0.0132

2.8980

68

N-069

Ar-NH2 / X-NH2

-0.3883

3.6841

69

N-070

Ar-NH-Al

-0.0389

4.2808

70

N-071

Ar-NAl2

0.1087

3.6189

71

N-072

RCO-N< / >N-X=X

-0.5113

2.5000

72

N-073

Ar2NH / Ar3N / Ar2N-Al / R..N..Rd

0.1259

2.7956

73

N-074

R#N / R=N-

0.1349

2.7000

74

N-075

R--N--Re / R--N--X

-0.1624

4.2063

75

N-076

Ar-NO2 / R--N(--R)--Of / RO-NO

-2.0585

4.0184

76

N-077

Al-NO2

-1.9150

3.0009

77

N-078

Ar-N=X / X-N=X

0.4208

4.7142

78

N-079

N+ (positively charged)

-1.4439

-

79

F-081

Fa attached to C1(sp3)

0.4797

0.8725

80

F-082

Fa attached to C2(sp3)

0.2358

1.1837

81

F-083

Fa attached to C3(sp3)

0.1029

1.1573

82

F-084

Fa attached to C1(sp2)

0.3566

0.8001

83

F-085

Fa attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X

0.1988

1.5013

84

Cl-086

Cla attached to C1(sp3)

0.7443

5.6156

85

Cl-087

Cla attached to C2(sp3)

0.5337

6.1022

86

Cl-088

Cla attached to C3(sp3)

0.2996

5.9921

87

Cl-089

Cla attached to C1(sp2)

0.8155

5.3885

88

Cl-090

Cla attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X

0.4856

6.1363

89

Br-091

Bra attached to C1(sp3)

0.8888

8.5991

90

Br-092

Bra attached to C2(sp3)

0.7452

8.9188

91

Br-093

Bra attached to C3(sp3)

0.5034

8.8006

92

Br-094

Bra attached to C1(sp2)

0.8995

8.2065

93

Br-095

Bra attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X

0.5946

8.7352

94

I-096

Ia attached to C1(sp3)

1.4201

13.9462

95

I-097

Ia attached to C2(sp3)

1.1472

14.0792

96

I-098

Ia attached to C3(sp3)

-

14.0730

97

I-099

Ia attached to C1(sp2)

0.7293

12.9918

98

I-100

Ia attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X

0.7173

13.3408

99

F-101

fluoride ion

-

-

100

Cl-102

chloride ion

-2.6737

-

101

Br-103

bromide ion

-2.4178

-

102

I-104

iodide ion

-3.1121

-

103

S-106

R-SH

0.6146

7.8916

104

S-107

R2S / RS-SR

0.5906

7.7935

105

S-108

R=S

0.8758

9.4338

106

S-109

R-SO-R

-0.4979

7.7223

107

S-110

R-SO2-R

-0.3786

5.7558

108

Si-111

>Si<

1.5188

-

109

B-112

>B- as in boranes

1.0255

-

110

P-115

P ylids

-

-

111

P-116

R3-P=X

-0.9359

5.5306

112

P-117

X3-P=X (phosphate)

-0.1726

5.5152

113

P-118

PX3 (phosphite)

-0.7966

6.8360

114

P-119

PR3 (phosphine)

0.6705

10.0101

115

P-120

C-P(X)2=X (phosphonate)

-0.4801

5.2806

 

▪R represents any group linked through carbon;
▪X represents any electronegative atom (O, N, S, P, Se, halogens);
▪Al and Ar represent aliphatic and aromatic groups, respectively;
▪= represents a double bond;
▪# represents a triple bond;
▪-- represents an aromatic bond as in benzene or delocalized bonds such as the N-O bond in a nitro group;
▪.. represents aromatic single bonds as the C – N bond in pyrrole.
▪a The superscript represents the formal oxidation number. The formal oxidation number of a carbon atom equals the sum of the conventional bond orders with electronegative atoms; the C--N bond order in pyridine may be considered as 2 while we have one such bond and 1.5 when we have two such bonds; the C..X bond order in pyrrole or furan may be considered as 1.
▪b An alpha-C may be defined as a C attached through a single bond with -C=X, -C#X, -C--X.
▪c As in nitro, N-oxides.
▪d Pyrrole-type structure.
▪e Pyridine-type structure.
▪f Pyridine N-oxide type structure.