Molecular properties

"The molecular descriptor is the final result of a logic and mathematical procedure which transforms chemical information encoded within a symbolic representation of a molecule into a useful number or the result of some standardized experiment." (Handbook of Molecular Descriptors, R.Todeschini and V.Consonni, Wiley-VCH, 2000).

 

Molecular descriptors play a fundamental role in chemistry, pharmaceutical sciences, environmental protection policy, health research and quality control, they being obtained when molecules are transformed into a molecular representation allowing some mathematical treatment. Many molecular descriptors have been proposed derived from different theories and approaches with the aim of predicting biological and physico-chemical properties of molecules [R.Todeschini and V.Consonni, Handbook of Molecular Descriptors, Wiley-VCH, Weinheim (GER), 2000].

 

The information content of a molecular descriptor depends on the kind of molecular representation that is used and on the defined algorithm for its calculation. There are simple molecular descriptors derived by counting some atom-types or structural fragments in the molecule, other derived from algorithms applied to a topological representation (molecular graph) and usually called topological or 2D-descriptors, and there are molecular descriptors derived from a geometrical representation that are called geometrical or 3D-descriptors.

 

All the molecular descriptors must contain, to varying extents, chemical information, must satisfy some basic invariance properties and general requirements, and must be derived from well-established procedures which enable molecular descriptors to be calculated for any set of molecules. It is obvious – almost trivial - that a single descriptor or a small number of descriptors cannot wholly represent the molecular complexity or model all the physico-chemical responses and biological interactions. As a consequence, although we must get used to living with approximate models (nothing is perfect!), we have to keep in mind that "approximate" is not a synonym of "useless".

 

The field of molecular descriptors is strongly interdisciplinary and involves a variety of different theories. For the definition of molecular descriptors, a knowledge of algebra, graph theory, information theory, computational chemistry, theories of organic reactivity and physical chemistry is usually required, although at different levels. For the use of the molecular descriptors, a knowledge of statistics, chemometrics, and the principles of the QSAR/QSPR approaches is necessary in addition to the specific knowledge of the problem.

 

The molecular descriptors/properties calculated by dProperties can be divided in three blocks:

1.Constitutional descriptors
2.Molecular properties
3.Drug-like indices

 

This is the complete list of calculated properties:

ID

Label   

Description

1

MW   

molecular weight

2

nAT

number of atoms

3

nBT

number of rotatable bonds

4

RBN   

number of rotatable bonds

5

nDB

number of double bonds

6

nAB

number of aromatic bonds

7

nH   

number of Hydrogen atoms

8

nC   

number of Carbon atoms

9

nN   

number of Nitrogen atoms

10

nO   

number of Oxygen atoms

11

nHet

number of heteroatoms

12

nX   

number of halogen atoms

13

nCIC   

number of rings (cyclomatic number)

14

nHDon   

number of donor atoms for H-bonds (N and O)

15

nHAcc   

number of acceptor atoms for H-bonds (N,O,F)

16

Uc   

unsaturation count

17

Ui   

unsaturation index

18

Hy   

hydrophilic factor

19

AMR   

Ghose-Crippen molar refractivity

20

TPSA(NO)   

topological polar surface area using N,O polar contributions

21

TPSA(Tot)   

topological polar surface area using N,O,S,P polar contributions

22

MLOGP   

Moriguchi octanol-water partition coeff. (logP)

23

MLOGP2   

squared Moriguchi octanol-water partition coeff. (logP2)

24

ALOGP   

Ghose-Crippen octanol-water partition coeff. (logP)

25

ALOGP2   

squared Ghose-Crippen octanol-water partition coeff. (logP2)

26

SAtot   

total surface area from P_VSA-like descriptors

27

SAacc   

surface area of acceptor atoms from P_VSA-like descriptors

28

SAdon   

surface area of donor atoms from P_VSA-like descriptors

29

Vx   

McGowan volume

30

VvdwMG   

van der Waals volume from McGowan volume

31

VvdwZAZ   

van der Waals volume from Zhao-Abraham-Zissimos equation

32

PDI   

packing density index

33

BLTF96   

Verhaar Fish base-line toxicity from MLOGP (mmol/l)

34

BLTD48   

Verhaar Daphnia base-line toxicity from MLOGP (mmol/l)

35

BLTA96   

Verhaar Algae base-line toxicity from MLOGP (mmol/l)

36

Ro5   

Lipinski Rule of 5

37

DLS_01   

modified drug-like score from Lipinski (4 rules)

38

DLS_02   

modified drug-like score from Oprea et al. (6 rules)

39

DLS_03   

modified drug-like score from Walters et al. (6 rules)

40

DLS_04   

modified drug-like score from Chen et al. (7 rules)

41

DLS_05   

modified drug-like score from Zheng et al. (2 rules)

42

DLS_06   

modified drug-like score from Rishton (6 rules)

43

DLS_07   

modified drug-like score from Veber et al. (2 rules)

44

DLS_cons   

DRAGON consensus drug-like score

45

LLS_01   

modified lead-like score from Congreve et al. (6 rules)

46

LLS_02   

modified lead-like score from Monge et al. (8 rules)

47

CMC-80   

Ghose-Viswanadhan-Wendoloski CMC drug-like index at 80%

48

CMC-50   

Ghose-Viswanadhan-Wendoloski CMC drug-like index at 50%

49

Inflammat-80   

Ghose-Viswanadhan-Wendoloski antiinflammatory-like index at 80%

50

Inflammat-50   

Ghose-Viswanadhan-Wendoloski antiinflammatory-like index at 50%

51

Depressant-80

Ghose-Viswanadhan-Wendoloski antidepressant-like index at 80%

52

Depressant-50 

Ghose-Viswanadhan-Wendoloski antidepressant-like index at 50%

53

Psychotic-80   

Ghose-Viswanadhan-Wendoloski antipsychotic-like index at 80%

54

Psychotic-50   

Ghose-Viswanadhan-Wendoloski antipsychotic-like index at 50%

55

Hypertens-80   

Ghose-Viswanadhan-Wendoloski antihypertensive-like index at 80%

56

Hypertens-50   

Ghose-Viswanadhan-Wendoloski antihypertensive-like index at 50%

57

Hypnotic-80   

Ghose-Viswanadhan-Wendoloski hypnotic-like index at 80%

58

Hypnotic-50   

Ghose-Viswanadhan-Wendoloski hypnotic-like index at 50%

59

Neoplastic-80   

Ghose-Viswanadhan-Wendoloski antineoplastic-like index at 80%

60

Neoplastic-50   

Ghose-Viswanadhan-Wendoloski antineoplastic-like index at 50%

61

Infective-80   

Ghose-Viswanadhan-Wendoloski antiinfective-like index at 80%

62

Infective-50   

Ghose-Viswanadhan-Wendoloski antiinfective-like index at 50%