P_VSA-like descriptors

These are molecular descriptors defined as the amount of van der Waals surface area (VSA) having a property P in a certain range [P.Labute, J. Mol. Graph. Model. 2000, 18, 464-477]. To generate P_VSA-like descriptors, first, the van der Waals surface area VSAi of each atom is estimated according to the following:

psva1

where R is the atomic van der Waals radius, the summation goes over all the atoms (nAT), but accounts only for contributions from atoms bonded to the ith atom, αij being the elements of the adjacency matrix. The quantity gij is calculated as:

psva2

where the term bij is the ideal length of the bond formed by atoms i and j, calculated according to the formula:

psva3

where rij is a reference bond length and cij a correction term depending on the bond multiplicity: 0 for single bond, 0.1 for aromatic, 0.2 for double, and 0.3 for triple bonds.

 

Van der Waals radii (in Angstrom) used for P_VSA-like descriptors

Atom-type

R

Atom-type

R

H (–O)

0.8

O (other)

1.779

H (–N, –P)

0.7

F

1.496

H (other)

1.485

P

2.287

C

1.950

S

2.185

N

1.950

Cl

2.044

O (oxide)

1.810

Br

2.166

O (acid)

2.152

I

2.358

 

Reference bond lengths (in Angstrom) used for P_VSA-like descriptors.

 

Bond-type

r*

Bond-type

r*

Br - Br

2.54

F - F

1.28

Br - C

1.97

F - H

0.87

Br - Cl

2.36

F - I

2.04

Br - F

1.85

F - N

1.41

Br - H

1.44

F - O

1.32

Br - I

2.65

F - P

1.5

Br - N

1.84

F - S

1.64

Br - O

1.58

H - I

1.63

Br - P

2.37

H - N

1.01

Br - S

2.21

H - O

0.97

C - C

1.54

H - P

1.41

C - Cl

1.8

H - S

1.31

C - F

1.35

I - I

2.92

C - H

1.06

I - N

2.26

C - I

2.12

I - O

2.14

C - N

1.47

I - P

2.49

C - O

1.43

I - S

2.69

C - P

1.85

N - N

1.45

C - S

1.81

N - O

1.46

Cl - Cl

2.31

N - P

1.6

Cl - F

1.63

N - S

1.76

Cl - H

1.22

O - O

1.47

Cl - I

2.56

O - P

1.57

Cl - N

1.74

O - S

1.57

Cl - O

1.41

P - P

2.26

Cl - P

2.01

P - S

2.07

Cl - S

2.07

S - S

2.05