Weighting schemes

Dragon makes use of some atomic properties as the atomic weighting schemes for molecular descriptor calculation. In order to select the weightings, click 'General settings' in the 'Settings' menu of the main menu bar. Then, in the tab 'Calculation' select the check boxes corresponding to the weightings to be used in descriptor calculation.

 

Note that:

1.the number of available molecular descriptors depends on the selected weighting schemes. Only the molecular descriptors that are based on the selected weighting schemes will be enabled in the window 'Select descriptors'.
2.the list of selected weightings is stored and will be used in successive work sessions of Dragon.
3.after each selection of weighting schemes, a new work session starts and previous results will be canceled.

 

Atomic properties used as the atomic weightings for descriptor calculation in Dragon are:

atomic mass (m);
van der Waals volume (v);
atom electronegativity (e);
atom polarizability (p);
ionization potential (i);
intrinsic state (s);

 

For each property, the unscaled and carbon atom scaled values can be seen in the window 'Weighting schemes' of the menu 'View' in the main menu bar.

For some molecular descriptors such as the WHIMs, another atomic weighting is derived from the electrotopological state indices of Kier and Hall (Kier, L.B., Hall, L.H. (1990), Pharm.Res., 7, 801-807). These are atomic indices calculated as:

 

In addition to the basic physico-chemical properties of atoms, Dragon implements calculation of molecular descriptors that are based on the intrinsic state. The intrinsic state (I-state) of the ith atom is a local vertex invariant calculated from the molecular graph as the following:

internal_structure_representation1

where L is the principal quantum number, δv is the number of valence electrons (valence vertex degree) and δ is the number of sigma electrons (simple vertex degree) of the ith atom in the H-depleted molecular structure. Since the I-state is only defined for non-H atoms, Dragon adopts the convention to use the value of 1 for hydrogens.

 

Data are taken from CRC Handbook of Chemistry and Physics by D.R. Lide (editor), CRC press 2009-2010, 90th edition.

 

Atomic No. (Z)

Atom

Mass (m)

Van der Waals volume (v)

Sanderson electroneg. (e)

Polarizability (p)

Ionization potential (i)

1

H

1.01

5.42

2.59

0.67

13.5984

2

He

4.003

11.49

n.a.

0.2

24.5874

3

Li

6.941

25.25

0.89

24.3

5.3917

4

Be

9.012

n.a.

1.81

5.6

9.3226

5

B

10.81

n.a.

2.28

3.03

8.298

6

C

12.01

20.58

2.75

1.76

11.2603

7

N

14.01

15.6

3.19

1.1

14.5341

8

O

16

14.71

3.65

0.8

13.6181

9

F

19

13.31

4

0.56

17.4228

10

Ne

20.18

15.3

4.5

0.39

21.5645

11

Na

22.991

49

0.56

23.6

5.1391

12

Mg

24.305

21.69

1.32

10.6

7.6462

13

Al

26.98

n.a.

1.71

6.8

5.9858

14

Si

28.09

38.79

2.14

5.38

8.1517

15

P

30.97

24.43

2.52

3.63

10.4867

16

S

32.07

24.43

2.96

2.9

10.36

17

Cl

35.45

22.45

3.48

2.18

12.9676

18

Ar

39.948

27.83

3.31

1.64

15.7596

19

K

39.098

87.11

0.45

43.4

4.3407

20

Ca

40.078

n.a.

0.95

22.8

6.1132

21

Sc

44.956

n.a.

1.02

17.8

6.5615

22

Ti

47.867

n.a.

1.09

14.6

6.8281

23

V

50.942

n.a.

1.39

12.4

6.7462

24

Cr

52

n.a.

1.66

11.6

6.7665

25

Mn

54.94

n.a.

2.2

9.4

7.434

26

Fe

55.85

n.a.

2.2

8.4

7.9024

27

Co

58.93

n.a.

2.56

7.5

7.881

28

Ni

58.69

18.14

1.94

6.8

7.6398

29

Cu

63.55

11.49

1.98

6.1

7.7264

30

Zn

65.39

11.25

2.23

7.1

9.3942

31

Ga

69.72

27.39

2.42

8.12

5.9993

32

Ge

72.61

n.a.

2.62

6.07

7.9

33

As

74.92

26.52

2.82

4.31

9.8152

34

Se

78.96

28.73

3.01

3.77

9.7524

35

Br

79.9

26.52

3.22

3.05

11.8138

36

Kr

83.8

34.53

2.91

2.48

13.9996

37

Rb

85.468

n.a.

0.31

47.3

4.1771

38

Sr

87.62

n.a.

0.72

27.6

5.6949

39

Y

88.906

n.a.

0.65

22.7

6.2173

40

Zr

91.224

n.a.

0.9

17.9

6.6339

41

Nb

92.906

n.a.

1.42

15.7

6.7589

42

Mo

95.94

n.a.

1.15

12.8

7.0924

43

Tc

98

n.a.

n.a.

11.4

7.28

44

Ru

101.07

n.a.

n.a.

9.6

7.3605

45

Rh

102.906

n.a.

n.a.

8.6

7.4589

46

Pd

106.42

18.14

n.a.

4.8

8.3369

47

Ag

107.87

21.31

1.83

7.2

7.5762

48

Cd

112.41

16.52

1.98

7.2

8.9938

49

In

114.82

30.11

2.14

10.2

5.7864

50

Sn

118.71

42.8

2.3

7.7

7.3438

51

Sb

121.76

n.a.

2.46

6.6

8.6084

52

Te

127.6

36.62

2.62

5.5

9.0096

53

I

126.9

32.52

2.78

5.35

10.4513

54

Xe

131.29

42.21

2.34

4.04

12.1298

55

Cs

132.905

n.a.

0.22

59.6

3.8939

56

Ba

137.327

n.a.

0.68

39.7

5.2117

57

La

138.906

n.a.

n.a.

31.1

5.5769

58

Ce

140.116

n.a.

n.a.

29.6

5.5387

59

Pr

140.908

n.a.

n.a.

28.2

5.473

60

Nd

144.24

n.a.

n.a.

31.4

5.525

61

Pm

145

n.a.

n.a.

30.1

5.55

62

Sm

150.36

n.a.

n.a.

28.8

5.6437

63

Eu

151.964

n.a.

n.a.

27.7

5.6704

64

Gd

157.25

n.a.

n.a.

23.5

6.1498

65

Tb

158.925

n.a.

n.a.

25.5

5.8639

66

Dy

162.5

n.a.

n.a.

24.5

5.9389

67

Ho

164.93

n.a.

n.a.

23.6

6.0215

68

Er

167.26

n.a.

n.a.

22.7

6.1077

69

Tm

168.934

n.a.

n.a.

21.8

6.1843

70

Yb

173.04

n.a.

n.a.

21

6.2542

71

Lu

174.967

n.a.

n.a.

21.9

5.4259

72

Hf

178.49

n.a.

n.a.

16.2

6.8251

73

Ta

180.948

n.a.

n.a.

13.1

7.5496

74

W

183.84

n.a.

0.98

11.1

7.864

75

Re

186.207

n.a.

n.a.

9.7

7.8335

76

Os

190.23

n.a.

n.a.

8.5

8.4382

77

Ir

192.217

n.a.

n.a.

7.6

8.967

78

Pt

195.08

21.31

n.a.

6.5

8.9588

79

Au

196.97

19.16

n.a.

5.8

9.2255

80

Hg

200.59

15.6

2.2

5.7

10.4375

81

Tl

204.38

31.54

2.25

7.6

6.1082

82

Pb

207.2

34.53

2.29

6.8

7.4166

83

Bi

208.98

n.a.

2.34

7.4

7.2855

84

Po

210

n.a.

n.a.

6.8

8.414

85

At

210

n.a.

n.a.

6

n.a.

86

Rn

222

n.a.

n.a.

5.3

10.7485

87

Fr

223

n.a.

n.a.

48.7

4.0727

88

Ra

226

n.a.

n.a.

38.3

5.2784

89

Ac

227

n.a.

n.a.

32.1

5.17

90

Th

232.038

n.a.

n.a.

32.1

6.3067

91

Pa

231.036

n.a.

n.a.

25.4

5.89

92

U

238.029

26.95

n.a.

27.4

6.1941

93

Np

237

n.a.

n.a.

24.8

6.2657

94

Pu

244

n.a.

n.a.

24.5

6.026

95

Am

243

n.a.

n.a.

23.3

5.9738

96

Cm

247

n.a.

n.a.

23

5.9914

97

Bk

247

n.a.

n.a.

22.7

6.1979

98

Cf

251

n.a.

n.a.

20.5

6.2817

99

Es

252

n.a.

n.a.

19.7

6.42

100

Fm

257

n.a.

n.a.

23.8

6.5

101

Md

258

n.a.

n.a.

18.2

6.58

102

No

259

n.a.

n.a.

17.5

6.65

103

Lr

262

n.a.

n.a.

n.a.

4.9

104

Rf

261

n.a.

n.a.

n.a.

6

105

Db

262

n.a.

n.a.

n.a.

n.a.

106

Sg

266

n.a.

n.a.

n.a.

n.a.

107

Bh

264

n.a.

n.a.

n.a.

n.a.

108

Hs

269

n.a.

n.a.

n.a.

n.a.

109

Mt

268

n.a.

n.a.

n.a.

n.a.

110

Ds

271

n.a.

n.a.

n.a.

n.a.

 

By clicking the upper right button icon_save_list in the window 'Weighting schemes' of the 'View' menu, a text file (.txt) can be generated with any name and storage location.