Message-ID: <1808976063.107.1632427486787.JavaMail.bigchem@cpu> Subject: Exported From Confluence MIME-Version: 1.0 Content-Type: multipart/related; boundary="----=_Part_106_1939211581.1632427486786" ------=_Part_106_1939211581.1632427486786 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Content-Location: file:///C:/exported.html Adriana.CODE

Adriana.CODE

N.B.! These descriptors can = be only used for model development on OCHEM web site and cannot be exported= .

ADRIANA.Code comprises a unique combination of met= hods for calculating molecular descriptors on a sound geometric and physico= chemical basis. These descriptors can be used for a wide range of applicati= ons in all areas of chemistry, in particular in QSAR/QSPR.
ADR= IANA.Code contains a series of methods for the generation of = 3D structures and the calculation of physicochemical descriptors and molecu= lar properties based on rapid empirical models. In addition, it contains a = hierarchy of increasing levels of sophistication in representing chemical c= ompounds from the constitution to the 3D structure of a molecule. At each l= evel, a wide range of physicochemical effects are included in the molecular= descriptors. 

Av= ailable descriptors

The following tables list the descriptors that are calculated by the OCH= EM web service of ADRIANA.Code.
For further deta= ils about the descriptors availaible in ADRIANA.Code,= their scientific and technical background and units, please refer to the&n= bsp;ADRIANA.Code = program manual. 

Global molecular descriptors

Global molecular descriptors represent a chemical structure by a structu= ral, chemical or physicochemical feature or property of the molecule expres= sed by a single value.
The total number of global molecular descriptor= s is 19.

Descriptor Short name in header line of cs= v descriptor file Unit References
Molecular weight Weight [u], [Da] [1]
Number of hydrogen bonding acceptors HAcc - [2]
Number of oxygen atom-based hydrogen bonding acc= eptors HAcc_O - [2]
Number of nitrogen atom-based hydrogen bonding a= cceptors HAcc_N - [2]
Number of hydrogen bonding donors HDon - [2]
Number of oxygen atom-based hydrogen bonding don= ors HDon_O - [2]
Number of nitrogen atom-based hydrogen bonding d= onors HDon_N - [2]
Octanol/water partition coefficient (logP) XlogP [log units] [3]
Topological polar surface area TPSA [Å2] [4]
Mean molecular polarizability Polariz [Å3] [5-8]
Molecular dipole moment Dipole [Debey] [9-15]
Aqueous solubility (logS) LogS [log units] [16]
Number of rotatable bonds NRotBond - [17]
Number of Ro5 violations NViolationsRo5 - [2]
Number of extended Ro5 violations NViolationsExtRo5 - [2]
Number of atoms NAtoms - -
Number of tetrahedral stereocenters NStereo - -
Molecular complexity Complexity - [18]
Ring complexity RComplexity - [19]

Shape and size descriptors

Shape and size descriptors characterize the size and the 3D shape of a m= olecule, e.g., if a molecule has a more enlongated or a spher= ical shape. These descriptors represent a molecule by a single value.
= The total number of shape- and size-related molecular descriptors is 8.

Descriptor Short name in header line of cs= v descriptor file Unit References
Molecular diameter Diameter [Å] [20]
Principal moment of inertia of 1st principal axi= s InertiaX [Da·Å2] [21]
Principal moment of inertia of 2nd principal axi= s InertiaX [Da·Å2] [21]
Principal moment of inertia of 3rd principal axi= s InertiaX [Da·Å2] [21]
Molecular span Span [Å] [22]
Molecular radius of gyration Rgyr [Å] [22-23]
Molecular eccentricity Eccentric [Å] [21]
Molecular asphericity Aspheric [Å] [21]

Topological or 2D property-weighted aut= ocorrelation descriptors

Topological or 2D property-weighted autocorrelation descriptors [24-25] = are calculated from 0 - 10 topological distances (i.e., the number= of bonds on the shortest path between two atoms), and sampled for each top= ological distance (11 distance bins). Thus, for each atom pair property a v= ector of 11 values (n) results.
The total number of 2D proper= ty-weighted autocorrelation descriptors is 88. The following table lists al= l 2D property-weighted autocorrelation descriptors.

Atom pair property Short name in header line of cs= v descriptor file References
Identity, i.e., "1" for = an atom 2DACorr_Ident_n -
=CF=83 charge 2DACorr_SigChg_n [10-11]
=CF=80 charge 2DACorr_PiChg_n [12-14]
Total charge 2DACorr_TotChg_n [10-14]
=CF=83 electronegativity 2DACorr_SigEN_n [10-11]
=CF=80 electronegativity 2DACorr_PiEN_n [12-14]
Lone-pair electronegativity 2DACorr_LpEN_n [12-14]
Effective atom polarizability 2DACorr_Polariz_n [5-8]

Spatial or 3D property-weighted autocorrela= tion descriptors

Spatial or 3D property-weighted autocorrelation descriptors [26-27] are = calculated from 1 - 13 Å and sampled in steps of 1 Å (12 distan= ce bins). Thus, for each atom pair property a vector of 12 values (n) results.
The total number of 3D property-weighted autocorrelation = descriptors is 96. The following table lists all 3D property-weighted autoc= orrelation descriptors.

Atom pair property Short name in header line of cs= v descriptor file References
Identity, i.e., "1" for = an atom 3DACorr_Ident_n -
=CF=83 charge 3DACorr_SigChg_n [10-11]
=CF=80 charge 3DACorr_PiChg_n [12-14]
Total charge 3DACorr_TotChg_n [10-14]
=CF=83 electronegativity 3DACorr_SigEN_n [10-11]
=CF=80 electronegativity 3DACorr_PiEN_n [12-14]
Lone-pair electronegativity 3DACorr_LpEN_n [12-14]
Effective atom polarizability 3DACorr_Polariz_n [5-8]

References

  1. Atomic weights were taken from www.webelements.com and are cur= rently implemented up to the atomic number of 109 (Mt, Meitnerium).
  2. Lipinski, C.A.; Lombardo, F.; Dominy, B.W.; Feeney, P.J. Experimental a= nd Computational Approaches to Estimate Solubility and Permeability in Drug= Discovery and Development Settings. Adv. Drug Delivery Rev.&= nbsp;1997, 23, 3-25.
  3. Wang, R.; Gao, Y; Lai, L. Calculating Partition Coefficient by Atom-Add= itive Method. Perspect. Drug Discovery Des. 2000= , 19, 47-66.
  4. Ertl, P; Rohde, B.; Selzer, P. Fast Calculation of Molecular Polar Surf= ace Area as a Sum of Fragment-Based Contributions and Its Application to th= e Prediction of Drug Tansport Properties. J. Med. Chem. = 2000, 43, 3714-3717.
  5. Gasteiger, J.; Hutchings, M.G. Empirical Models of Substituent Polarisa= bility and their Application to Stabilisation Effects in Positively Charged= Species. Tetrahedron Lett. 1983, = 24, 2537-2540.
  6. Gasteiger, J.; Hutchings, M.G. Quantitative Models of Gas-Phase Proton = Transfer Reactions Involving Alcohols, Ethers and their Thio Analogs. Corre= lation Analyses Based on Residual Electronegativity and Effective Polarizab= ility. J. Am. Chem. Soc. 1984, 106, 6489-6495.
  7. Kang, Y.K.; Jhon, M.S. Theor. Chim. Acta 198= 2, 61, 41.
  8. Miller, K.J. Additivity Methods in Molecular Polarizability. J= . Am. Chem. Soc. 1990, 112, 8533-8= 542.
  9. (a) Sadowski, J.; Gasteiger, J.; Klebe, G. Comparison of Automatic Thre= e-Dimensional Model Builders Using 639 X-Ray Structures. J. Chem. = Inf. Comput. Sci. 1994, 34, 1000-1= 008.
    10. (b) CORINA by Molecular Networks GmbH, Erlangen, Germany.
  10. (a) Hinze, J.; Jaffe, H.H. J. Am. Chem. Soc. 1962, 84, 540. (b) Hinze, J.; Jaffe, H.H. = J. Am. Chem. Soc. 1963, 85, 148. (= c) Hinze, J.; Jaffe, H.H. J. Phys. Chem. 1963, 67, 1501.
  11. (a) Gasteiger, J.; Marsili, M. A New Model for Calculating Atomic Charg= es in Molecules. Tetrahedron Lett. 1978= , 34, 3181-3184. (b) Gasteiger, J.; Marsili, M. Iterative Par= tial Equalization of Orbital Electronegativity - A Rapid Access to Atomic C= harges. Tetrahedron 1980, 36, 3219-3228. (c) Gasteiger, J.; Guillen, M.D. Extension of the Method of= Iterative Partial Equalization of Orbital Electronegativity to Small Ring = Systems. Tetrahedron 1983, 39<= /em>, 1331-1335.
  12. Bauerschmidt, S.; Gasteiger J. Overcoming the Limitations of a Connecti= on Table Description: A Universal Representation of Chemical Species. = J. Chem. Inf. Comput. Sci. 1997, 37= , 705-714.
  13. Streitwieser, A. Jr. Molecular Orbital Theory for Organic Chem= ists. John Wiley & Sons, Inc. New York, London: 1961.
  14. (a) Abraham, R.J.; Hudson, B. J. Comp. Chem. 1984, 6, 562-570. (b) Abraham, R.J.; Hudson, B.&nbs= p;J. Comp. Chem. 1985, 6, 173-= 181. (c) Abraham, R.J.; Smith, P.E. J. Comp. Chem. 1987, 9, 288-297.
  15. (a) Saller, H.; Gasteiger, J. Calculation of the Charge Distribution in= Conjugated Systems by a Quantification of the Resonance Concept. = Angew. Chem. Int. Ed. Engl. 1985, 24, 687-689. (b) Saller, H.; Gasteiger, J. Berechnung der Ladungsverteilung= in konjugierten Systemen durch eine Quantifizierung des Mesomeriekonzeptes= . Angew. Chem. 1985, 97, = 699-701.
  16. (a) Yan, A.; Gasteiger, J. Prediction of Aqueous Solubility of Organic = Compounds Based on a 3D Structure Representation. J. Chem. Inf. Co= mput. Sci. 2003, 43, 429-434. (b) = Yan, A.; Gasteiger, J.; Krug, M.; Anzali, S. Linear and Nonlinear Functions= on Modeling the Aqueous Solubility of Organic Compounds by Two Structure R= epresentation Methods. J. Comput.-Aided Mol. Design 2004, 18, 75-87. (c) Schmid, B. Deriving a Linea= r Model for Predicting the Solubility Coefficient for Organic Molecules.&nb= sp;Personal Communications 2005.
  17. Veber, D.F.; Johnson, S.R.; Cheng, H.-Y.; Smith, B.R.; Ward, K.W.; Kopp= le, K.D. Molecular Properties That Influence the Oral Bioavailability of Dr= ug Candidates. J. Med. Chem. 2002, = ;45 (12), 2615-2623.
  18. Hendrickson, J.B.; Huang, P.; Toczko, A.G. Molecular Complexity: A Simp= lified Formula Adapted to Individual Atoms. J. Chem. Inf. Comput. = Sci. 1987, 27, 63-67.
  19. Gasteiger, J; Jochum, C. An Algorithm for the Perception of Synthetical= ly Important Rings. J. Chem. Inf. Comput. Sci. 1= 979, 19, 43-48.
  20. Petitjean, M. Applications of the radius-diameter diagram to the classi= fication of topological and geometrical shapes of chemical compounds. = J. Chem. Inf. Comput. Sci. 1992, 32= , 331-337.
  21. Todeschini, R.; Consonni, V. Handbook of Molecular Descriptors= . Wiley-VCH, Weinheim: 2000, Vol. 11.
  22. Volkenstein, M.V. Configurational Statistics of Polymeric Chai= ns. Wiley-Interscience, New York: 1963.
  23. Tanford, C. Physical Chemistry of Macromolecules. Wi= ley, New York: 1961.
  24. (a) Moreau, G.; Broto, P. Nouv. J. Chim. 198= 0, 4, 359-360. (b) Broto, P.; Moreau, G.; Vandycke, = C. Eur. J. Med. Chem. Chim. Ther. 1984,=  19, 66-70.
  25. Bauknecht, H.; Zell, A.; Bayer, H.; Levi, P.; Wagener, M.; Sadowski, J.= ; Gasteiger, J. Locating Biologically Active Compounds in Medium-Sized Hete= rogeneous Datasets by Topological Autocorrelation Vectors: Dopamine and Ben= zodiazepine Agonists. J. Chem. Inf. Comput. Sci. 1996, 36, 1205-1213.
  26. (a) Wagener, M.; Sadowski, J.; Gasteiger, J. Assessing the Similarity a= nd Diversity of Combinatorial Libraries by Spatial Autocorrelation Function= s and Neural Networks. Angew. Chem. Int. Ed. Engl.199= 5, 34, 2674-2677. (b) Wagener, M.; Sadowski, J.; Gas= teiger, J. Bewertung der Ähnlichkeit und Vielfalt von Verbindungsbibli= otheken mit räumlichen Autokorrelationsvektoren und neuronalen Netzen.= Angew. Chem. 1995, 107, 2892-2= 895.
  27. Teckentrup, A.; Briem, H.; Gasteiger, J. Mining High-Throughput Screeni= ng Data of Combinatorial Libraries: Development of a Filter to Distinguish = Hits from Nonhits. J. Chem. Inf. Comput. Sci. 20= 04,44, 626-634.

Copy= right statement

ADRIANA is a registered trademark owned by Molecul= ar Networks GmbH, Erlangen, Germany in the Federal Republic of Germany. Oth= er product names and company names may be trademarks or registered trademar= ks of their respective owners, in the Federal Republic of Germany and other= countries. All rights reserved.

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