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propertieschemaxon [2012/10/11 22:38] – created rkisspropertieschemaxon [2012/11/07 16:09] – rkiss
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 ====== ChemAxon properties ====== ====== ChemAxon properties ======
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-ChemAxon’s widely used Calculator Plugins have been developed and optimized for many years and the calculated physicochemical properties show good correlation with experimental results. 
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-To get access to ChemAxon properties, subscribe to ChemAxon Properties Access (link). Note that the Access package option is free for academic users. 
- 
-More information about ChemAxon Calculator Plugins: 
-http://www.chemaxon.com/marvin/help/calculations/calculator-plugins.html 
  
 **logP:** Logarithm of the octanol/water partition coefficient **logP:** Logarithm of the octanol/water partition coefficient
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 **Atoms:** Number of atoms **Atoms:** Number of atoms
  
-Carbon atoms: Number of carbon atoms+**Carbon atoms:** Number of carbon atoms
  
-Nitrogen atoms: Number of nitrogen atoms+**Nitrogen atoms:** Number of nitrogen atoms
  
-Oxygen atoms: Number of oxygen atoms+**Oxygen atoms:** Number of oxygen atoms
  
-N/O atoms: Number of nitrogen and oxygen atoms+**N/O atoms:** Number of nitrogen and oxygen atoms
  
-Exact mass: Monoisotopic molecular mass calculated from the atomic masses of the most frequent natural isotopes+**Exact mass:** Monoisotopic molecular mass calculated from the atomic masses of the most frequent natural isotopes
  
-Mass: Average molecular mass calculated from the atomic masses of all isotopes weighted by their natural occurrence+**Mass:** Average molecular mass calculated from the atomic masses of all isotopes weighted by their natural occurrence
  
-Molecular polarizability: Molecular polarizability calculated from atomic contributions+**Molecular polarizability:** Molecular polarizability calculated from atomic contributions
  
-Molecular polarizability (at pH=7.4): Molecular polarizability of the major microspecies at pH=7.4 calculated from atomic contributions+**Molecular polarizability (at pH=7.4):** Molecular polarizability of the major microspecies at pH=7.4 calculated from atomic contributions
  
-Aliphatic atoms: Number of aliphatic atoms+**Aliphatic atoms:** Number of aliphatic atoms
  
-Aliphatic bonds: Number of aliphatic bonds+**Aliphatic bonds:** Number of aliphatic bonds
  
-Aliphatic rings: Number of aliphatic rings+**Aliphatic rings:** Number of aliphatic rings
  
-Aliphatic 3-membered rings: Number of aliphatic 3-membered rings+**Aliphatic 3-membered rings:** Number of aliphatic 3-membered rings
  
-Aliphatic 4-membered rings: Number of aliphatic 4-membered rings+**Aliphatic 4-membered rings:** Number of aliphatic 4-membered rings
  
-Aliphatic 5-membered rings: Number of aliphatic 5-membered rings+**Aliphatic 5-membered rings:** Number of aliphatic 5-membered rings
  
-Aliphatic 6-membered rings: Number of aliphatic 6-membered rings+**Aliphatic 6-membered rings:** Number of aliphatic 6-membered rings
  
-Aliphatic 7-membered rings: Number of aliphatic 7-membered rings+**Aliphatic 7-membered rings:** Number of aliphatic 7-membered rings
  
-Aliphatic 8-membered rings: Number of aliphatic 8-membered rings+**Aliphatic 8-membered rings:** Number of aliphatic 8-membered rings
  
-Aromatic atoms: Number of aromatic atoms+**Aromatic atoms:** Number of aromatic atoms
  
-Aromatic bonds: Number of aromatic bonds+**Aromatic bonds:** Number of aromatic bonds
  
-Aromatic rings: Number of aromatic rings+**Aromatic rings:** Number of aromatic rings
  
-Aromatic 3-membered rings: Number of aromatic 3-membered rings+**Aromatic 3-membered rings:** Number of aromatic 3-membered rings
  
-Aromatic 4-membered rings: Number of aromatic 4-membered rings+**Aromatic 4-membered rings:** Number of aromatic 4-membered rings
  
-Aromatic 5-membered rings: Number of aromatic 5-membered rings+**Aromatic 5-membered rings:** Number of aromatic 5-membered rings
  
-Aromatic 6-membered rings: Number of aromatic 6-membered rings+**Aromatic 6-membered rings:** Number of aromatic 6-membered rings
  
-Aromatic 7-membered rings: Number of aromatic 7-membered rings+**Aromatic 7-membered rings:** Number of aromatic 7-membered rings
  
-Aromatic 8-membered rings: Number of aromatic 8-membered rings+**Aromatic 8-membered rings:** Number of aromatic 8-membered rings
  
-ASA (at pH=7.4): Total solvent accessible surface area (in Angstrom2) of major microspecies at pH=7.4+**ASA (at pH=7.4):** Total solvent accessible surface area (in Angstrom<sup>2</sup>) of major microspecies at pH=7.4
  
-ASA+ (at pH=7.4): Solvent accessible surface area (in Angstrom2) of all atoms with positive partial charge of major microspecies at pH=7.4+**ASA+ (at pH=7.4):** Solvent accessible surface area (in Angstrom<sup>2</sup>) of all atoms with positive partial charge of major microspecies at pH=7.4
  
-ASA- (at pH=7.4): Solvent accessible surface area (in Angstrom2) of all atoms with negative partial charge of major microspecies at pH=7.4+**ASA- (at pH=7.4):** Solvent accessible surface area (in Angstrom<sup>2</sup>) of all atoms with negative partial charge of major microspecies at pH=7.4
  
-ASA_H (at pH=7.4): Solvent accessible surface area (in Angstrom2) of all hydrophobic (|qi|<0.125) atoms (|qi| is the absolute value of the partial charge of the atom) of major microspecies at pH=7.4+**ASA_H (at pH=7.4):** Solvent accessible surface area (in Angstrom<sup>2</sup>) of all hydrophobic (|qi|<0.125) atoms (|qi| is the absolute value of the partial charge of the atom) of major microspecies at pH=7.4
  
-ASA_P (at pH=7.4): Solvent accessible surface area (in Angstrom2) of all polar (|qi|>0.125) atoms (|qi| is the absolute value of the partial charge of the atom) of major microspecies at pH=7.4+**ASA_P (at pH=7.4):** Solvent accessible surface area (in Angstrom<sup>2</sup>) of all polar (|qi|>0.125) atoms (|qi| is the absolute value of the partial charge of the atom) of major microspecies at pH=7.4
  
-ASA: Total solvent accessible surface area (in Angstrom2)+**ASA:** Total solvent accessible surface area (in Angstrom<sup>2</sup>)
  
-ASA+: Solvent accessible surface area (in Angstrom2) of all atoms with positive partial charge+**ASA+:** Solvent accessible surface area (in Angstrom<sup>2</sup>) of all atoms with positive partial charge
  
-ASA-: Solvent accessible surface area (in Angstrom2) of all atoms with negative partial charge+**ASA-:** Solvent accessible surface area (in Angstrom<sup>2</sup>) of all atoms with negative partial charge
  
-ASA_H: Solvent accessible surface area (in Angstrom2) of all hydrophobic (|qi|<0.125) atoms (|qi| is the absolute value of the partial charge of the atom)+**ASA_H:** Solvent accessible surface area (in Angstrom<sup>2</sup>) of all hydrophobic (|qi|<0.125) atoms (|qi| is the absolute value of the partial charge of the atom)
  
-ASA_P: Solvent accessible surface area (in Angstrom2) of all polar (|qi|>0.125) atoms (|qi| is the absolute value of the partial charge of the atom)+**ASA_P:** Solvent accessible surface area (in Angstrom<sup>2</sup>) of all polar (|qi|>0.125) atoms (|qi| is the absolute value of the partial charge of the atom)
  
-Asymmetric atoms: Number of asymmetric atoms+**Asymmetric atoms:** Number of asymmetric atoms
  
-Balaban index: Balaban distance connectivity, which is the average distance sum connectivity+**Balaban index:** Balaban distance connectivity, which is the average distance sum connectivity
  
-Bonds: Number of bonds including bonds of hydrogen atoms+**Bonds:** Number of bonds including bonds of hydrogen atoms
  
-Carbon rings: Number of rings containing carbon atoms only+**Carbon rings:** Number of rings containing carbon atoms only
  
-Aliphatic carbon rings: Number of aliphatic rings containing carbon atoms only+**Aliphatic carbon rings:** Number of aliphatic rings containing carbon atoms only
  
-Aromatic carbon rings: Number of aromatic rings containing carbon atoms only+**Aromatic carbon rings:** Number of aromatic rings containing carbon atoms only
  
-Chain atoms: Number of chain atoms (non-ring atoms excluding hydrogens)+**Chain atoms:** Number of chain atoms (non-ring atoms excluding hydrogens)
  
-Chain bonds: Number of chain bonds (non-ring bonds excluding bonds of hydrogen atoms)+**Chain bonds:** Number of chain bonds (non-ring bonds excluding bonds of hydrogen atoms)
  
-Chiral centers: Number of tetrahedral stereogenic center atoms.+**Chiral centers:** Number of tetrahedral stereogenic center atoms.
  
-Cyclomatic number: Smallest number of bonds which must be removed so that no circuit remains. Also known as circuit rank.+**Cyclomatic number:** Smallest number of bonds which must be removed so that no circuit remains. Also known as circuit rank.
  
-Fused aliphatic rings: Number of fused aliphatic rings+**Fused aliphatic rings:** Number of fused aliphatic rings
  
-Fused aromatic rings: Number of fused aromatic rings+**Fused aromatic rings:** Number of fused aromatic rings
  
-Fused rings: Number of fused rings+**Fused rings:** Number of fused rings
  
-Harary index: Half-sum of the off-diagonal elements of the reciprocal molecular distance matrix+**Harary index:** Half-sum of the off-diagonal elements of the reciprocal molecular distance matrix
  
-Hetero aliphatic rings: Number of aliphatic heterocycles+**Hetero aliphatic rings:** Number of aliphatic heterocycles
  
-Hetero aromatic rings: Number of aromatic heterocycles+**Hetero aromatic rings:** Number of aromatic heterocycles
  
-Hetero rings: Number of heterocycles+**Hetero rings:** Number of heterocycles
  
-Hyper Wiener index: A variant of the Wiener index+**Hyper Wiener index:** A variant of the Wiener index
  
-Largest ring size: Size of the largest ring+**Largest ring size:** Size of the largest ring
  
-Largest ring system size: Number of rings in the +**Largest ring system size:** Number of rings in the 
 largest ring system largest ring system
  
-VdWSA (at pH=7.4): Van der Waals surface area of the major microspecies at pH=7.4+**VdWSA (at pH=7.4):** Van der Waals surface area of the major microspecies at pH=7.4
  
-VdWSA: Van der Waals surface area+**VdWSA:** Van der Waals surface area
  
-Platt index: Sum of the edge degrees of a molecular graph+**Platt index:** Sum of the edge degrees of a molecular graph
  
-PSA (at pH=7.4): Topological polar surface area of the major microspecies at pH=7.4+**PSA (at pH=7.4):** Topological polar surface area of the major microspecies at pH=7.4
  
-PSA: Topological polar surface area+**PSA:** Topological polar surface area
  
-Randic index: Harmonic sum of the geometric means of the node degrees for each edge+**Randic index:** Harmonic sum of the geometric means of the node degrees for each edge
  
-Ring atoms: Number of ring atoms+**Ring atoms:** Number of ring atoms
  
-Ring bonds: Number of ring bonds+**Ring bonds:** Number of ring bonds
  
-Rings: Number of rings (smallest set of smallest rings)+**Rings:** Number of rings (smallest set of smallest rings)
  
-3-membered rings: Number of 3-membered rings+**3-membered rings:** Number of 3-membered rings
  
-4-membered rings: Number of 4-membered rings+**4-membered rings:** Number of 4-membered rings
  
-5-membered rings: Number of 5-membered rings+**5-membered rings:** Number of 5-membered rings
  
-6-membered rings: Number of 6-membered rings+**6-membered rings:** Number of 6-membered rings
  
-7-membered rings: Number of 7-membered rings+**7-membered rings:** Number of 7-membered rings
  
-8-membered rings: Number of 8-membered rings+**8-membered rings:** Number of 8-membered rings
  
-Ring systems: Number of disjunct ring systems+**Ring systems:** Number of disjunct ring systems
  
-Rotatable bonds: Number of rotatable bonds+**Rotatable bonds:** Number of rotatable bonds
  
-Smallest ring size: Size of the smallest ring+**Smallest ring size:** Size of the smallest ring
  
-Smallest ring system size: Number of rings in the +**Smallest ring system size:** Number of rings in the 
 smallest ring system smallest ring system
  
-Cis-trans stereo double bonds: Number of double bonds with defined cis or trans stereochemistry+**Cis-trans stereo double bonds:** Number of double bonds with defined cis or trans stereochemistry
  
-Szeged index: Wiener index extended for cyclic graphs by counting the number of atoms on both sides of each bond (those atoms only which are nearer to the given side of the bond than to the other), and sum these counts.+**Szeged index:** Wiener index extended for cyclic graphs by counting the number of atoms on both sides of each bond (those atoms only which are nearer to the given side of the bond than to the other), and sum these counts.
  
-Wiener index: Average topological atom distance (half of the sum of all atom distances)+**Wiener index:** Average topological atom distance (half of the sum of all atom distances)
  
-Wiener polarity: Number of 3 bond length distances+**Wiener polarity:** Number of 3 bond length distances
  
-Double bond stereoisomers: Number of double bond stereoisomers+**Double bond stereoisomers:** Number of double bond stereoisomers
  
-Stereoisomers: Number of stereoisomers+**Stereoisomers:** Number of stereoisomers
  
-Tautomers (at pH=7.4): Number of dominant tautomers at pH=7.4+**Tautomers (at pH=7.4):** Number of dominant tautomers at pH=7.4
  
-Tetrahedral stereoisomers: Number of tetrahedral stereoisomers+**Tetrahedral stereoisomers:** Number of tetrahedral stereoisomers
  
-H-bond acceptors: Number of hydrogen bond acceptor atoms+**H-bond acceptors:** Number of hydrogen bond acceptor atoms
  
-H-bond acceptors (at pH=7.4): Number of hydrogen bond acceptor atoms of the major microspecies at pH=7.4+**H-bond acceptors (at pH=7.4):** Number of hydrogen bond acceptor atoms of the major microspecies at pH=7.4
  
-H-bond acceptor sites: Number of hydrogen bond acceptor sites+**H-bond acceptor sites:** Number of hydrogen bond acceptor sites
  
-H-bond acceptor sites (at pH=7.4): Number of hydrogen bond acceptor sites of the major microspecies at pH=7.4+**H-bond acceptor sites (at pH=7.4):** Number of hydrogen bond acceptor sites of the major microspecies at pH=7.4
  
-H-bond donors: Infobox: Number of hydrogen bond donor atoms+**H-bond donors:** Number of hydrogen bond donor atoms
  
-H-bond donors (at pH=7.4): Number of hydrogen bond donor atoms of the major microspecies at pH=7.4”+**H-bond donors (at pH=7.4):** Number of hydrogen bond donor atoms of the major microspecies at pH=7.4
  
-H-bond donor sites: Number of hydrogen bond donor sites+**H-bond donor sites:** Number of hydrogen bond donor sites
  
-H-bond donor sites (at pH=7.4): Number of hydrogen bond donor sites of the major microspecies at pH=7.4+**H-bond donor sites (at pH=7.4):** Number of hydrogen bond donor sites of the major microspecies at pH=7.4
  
-HMO Pi energy: Pi energy of the aromatic ring(s) (dimension beta)+**HMO Pi energy:** Pi energy of the aromatic ring(s) (dimension beta)
  
-HMO Pi energy (at pH=7.4): Pi energy of the aromatic ring(s) (dimension beta) of the major microspecies at pH=7.4+**HMO Pi energy (at pH=7.4):** Pi energy of the aromatic ring(s) (dimension beta) of the major microspecies at pH=7.4
  
-Refractivity: Molar refractivity+**Refractivity:** Molar refractivity
  
-Resonants: Number of resonance structures+**Resonants:** Number of resonance structures
  
-RO5 violations (at pH=7.4): Number of rule-of-five (Lipinski) violations of the major microspecies at pH=7.4+**RO5 violations (at pH=7.4):** Number of [[http://en.wikipedia.org/wiki/Rule_of_five|rule-of-five]] violations of the major microspecies at pH=7.4
  
-RO5 violations: Number of rule-of-five (Lipinski) violations+**RO5 violations:** Number of [[http://en.wikipedia.org/wiki/Rule_of_five|rule-of-five]] violations
  
-RO3 violations (at pH=7.4): Number of rule-of-three (Astex) violations of the major microspecies at pH=7.4+**RO3 violations (at pH=7.4):** Number of [[http://www.nature.com/nrd/journal/v3/n8/box/nrd1467_BX1.html|rule-of-three]] violations of the major microspecies at pH=7.4
  
-RO3 violations: Number of rule-of-three (Astex) violations+**RO3 violations:** Number of [[http://www.nature.com/nrd/journal/v3/n8/box/nrd1467_BX1.html|rule-of-three]] violations