University of Tuebingen Lehrstuhl Kognitive Systeme, Prof Dr. Zell
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Atom properties

The formal definition of atom properties is given in chapter Chapter 2.

Atom in acceptor

Is this atom a hydrogen acceptor atom αacceptor(G,V,Achem|JOELib,kernelID). We used here the interpretation of Böhm/Klebe [bk02].

Atom in conjugated environment

Atom in conjugated environment αconj(G,V,Achem|JOELib,kernelID) [wfz04a,wfz04b,fwz04].

Table 5-1. SMARTS definitions for assigning the conjugated atom property flag

SMARTSDescription
aAromatic atoms
*=,#*-,=*=,#*All butadien analogues
[N,P,O,S]=,#*-[*;!H0]alpha, beta unsaturated (pi effect)
*=,#*-[F,Cl,Br,I]alpha, beta unsaturated (sigma effect)
*=,#*-[N,P,O,S;!H0]alpha, beta unsaturated (pi effect, tautomer)

Atom in donor or acceptor

Is this atom a hydrogen donor or acceptor atom αdon,acc(G,V,Achem|JOELib,kernelID). We used here the interpretation of Böhm/Klebe [bk02].

Atom in donor

Is this atom a hydrogen donor atom αdonor(G,V,Achem|JOELib,kernelID). We used here the interpretation of Böhm/Klebe [bk02].

Atom in ring

Is this atom a ring atom αinRing(G,V,Achem|JOELib,kernelID).

Atom is terminal carbon

Is this atom a terminal carbon atom αmethylen(G,V,Achem|JOELib,kernelID).

Atom is negative

Is this atom a negative charged atom αnegative(G,V,Achem|JOELib,kernelID).

Atom is positive

Is this atom a positive charged atom αpositive(G,V,Achem|JOELib,kernelID).

Atom masss

Atom mass.

Valence

Valence.

Van der Waals volume

Van der Waals volume.

Conjugated electrotopological state

Conjugated electrotopological state [wz03,wfz04b].

Equation 5-7. Conjugated electrotopological state

Ii is the intrinsic state of atom i (the Section called Intrinsic topological state) and k the distance influence. The distance influence is reduced by the conjugated topological distance

Equation 5-8. Conjugated topological distance

where Ci is the conjugated atom i (the Section called Atom in conjugated environment) of the molecule.

Electrogeometrical state

Electrogeometrical state αEGstate(G,V,Achem|JOELib,kernelID) [wz03,wfz04b].

Equation 5-9. Electrogeometrical state

Ii is the intrinsic state of atom i (the Section called Intrinsic topological state) and k the distance influence.

Electron affinity

Electron affinity.

Electronegativity after Pauling

Electronegativity after Pauling.

Electrotopological state

Electrotopological state αEstate(G,V,Achem|JOELib,kernelID) [tc00,wfz04b].

Equation 5-10. Electrotopological state

Ii is the intrinsic state of atom i (the Section called Intrinsic topological state) and k the distance influence.

Gasteiger-Marsili

Calculation of atom partial charges (Gasteiger-Marsili) αGM(G,V,Achem|JOELib,kernelID) [gm78]. The Partial Equalization of Orbital Electronegativities (PEOE) sigma charges of atoms can be calculated using an iterative algorithm. There exists a dependency between the electronegativity χi,A and the charge qA of an atom:

Equation 5-11. Orbital electronegativity based on atom charge

where i is the orbital and A the atom.

The algorithm requires the polynomial coefficients ai, bi, ci the damping factor α and the maximal number of iterations Nmax. Because the amount of charge transferred at each iteration is damped with an exponentially decreasing factor the convergence is guaranteed.

Graph potentials

Graph potentials αGP(G,V,Achem|JOELib,kernelID) [wy96] or rotational symmetry descriptor. Only the connection table is needed to calculate the external rotational symmetry, or topological equivalent atoms.

Equation 5-12. Graph potentials

where vi is the valence (vertex degree) of the atom i.

Intrinsic topological state

Intrinsic topological state αIstate(G,V,Achem|JOELib,kernelID) [tc00,wfz04b].

Equation 5-13. Intrinsic topological state

where Li is the principal quantum number, δiν is the number of valence electrons, and δi is the number of sigma electrons of the ith atom ai.


Last changes: 08.12.2010, 16:50 CET (UTC/GMT +1 hour) wegner.
http://www.ra.cs.uni-tuebingen.de/software/joelib/tutorial/descriptors/atomProperties.html
2003 University of Tübingen, Germany