Principal Moment of Intertia (PMI)-Derived Properties

This node calculates Principal Moment of Intertia (PMI)-Derived Properties

The properties are:

  • PMI 1 - First (smallest) Principal Moment of Inertia (also referred to as: I₁)
  • PMI 2 - Second Principal Moment of Inertia (also referred to as: I₂)
  • PMI 3 - Third (largest) Principal Moment of Inertia (also referred to as: I₃)
  • npr1 - First Normalised PMI (i.e. I₁ / I₃) (See: Sauer and Schwartz, J. Chem. Inf. Comput. Sci., 2003, 43, 987-1003)
  • npr2 - Second Normalised PMI (i.e. I₂ / I₃) (See: Sauer and Schwartz, J. Chem. Inf. Comput. Sci., 2003, 43, 987-1003)
  • Sigma npr - npr1 + npr2 (also referred to as: Flatsum, npr1+npr2, Σnpr) (See: )
  • Sphericity - npr1 + npr2 - 1 (also referred to as: S) (See: Wirth et al., J. Comput. Aided Mol. Des., 2013, 27, 511-524)
  • Rodlikeness - npr2 - npr1 (also referred to as: R, Rod-likeness) (See: Wirth et al., J. Comput. Aided Mol. Des., 2013, 27, 511-524)
  • Disklikeness - 2 - 2 × npr2 (also referred to as: D, Disc-likeness) (See: Wirth et al., J. Comput. Aided Mol. Des., 2013, 27, 511-524)
  • Asphericity - 0.5 × [(I₁ - I₂)² + (I₁ - I₃)² + (I₂ - I₃)²]/[I₁² + I₂² + I₃²]; 0 corresponds to a spherical top and 1 to a linear molecule. ~0.25 corresponds to prolate (cigar-shaped) molecules, and disc-shaped ~1 (also referred to as: ΩA) (See: Arteca, Reviews in Computational Chemistry, Vol 9 VCH, NY, 1991, 191-253)
  • Inertial Shape Factor - I₂ / (I₁ × I₃); Undefined for planar molecules (also referred to as: S<sub>I</sub>) (See: Lister et al., Internal Rotation and Inversion, Academic Press, London, 1978)
  • Molecule Eccentricity - √(I₁² - I₃²) / I₂; 0 corresponds to a spherical top, and 1 to a linear molecule (also referred to as: ε) (See: Arteca, Reviews in Computational Chemistry, Vol 9 VCH, NY, 1991, 191-253)
  • Gyradius - Radius of Gyration (also referred to as: RG, Radius of Gyration, Gyradius) (See: )
  • Gyradius 2D - Radius of Gyration (2D) = √(I₁ × I₂) / MWt (also referred to as: RG, Radius of Gyration, Gyradius) (See: Volkenstein 'Configurational Statistics of Polymeric chains' Wiley, NY, 1963)
  • Gyradius 3D - Radius of Gyration (3D) = ∛(I₁ × I₂ × I₃) / MWt (also referred to as: RG, Radius of Gyration, Gyradius) (See: Tanford 'Physical Chemistry of Macromolecules', Wiley, NY, 1961)
  • PRG 0 - 1st Principle Radius of Gyration (R0 = √(I₁ / MWt)) (also referred to as: R0) (See: Jian et al., 'A dimension map for molecular aggregates', J. Mol. Graphics. Model., 2015, 58, 10-15)
  • PRG 1 - 2nd Principle Radius of Gyration (R1 = √(I₂ / MWt)) (also referred to as: R1) (See: Jian et al., 'A dimension map for molecular aggregates', J. Mol. Graphics. Model., 2015, 58, 10-15)
  • PRG 2 - 3rd Principle Radius of Gyration (R2 = √(I₃ / MWt)) (also referred to as: R2) (See: Jian et al., 'A dimension map for molecular aggregates', J. Mol. Graphics. Model., 2015, 58, 10-15)
  • Gyradius Ratio 1 - 1st Gyradius Ratio (r1 = PRG1 / PRG0) (also referred to as: r1) (See: Jian et al., 'A dimension map for molecular aggregates', J. Mol. Graphics. Model., 2015, 58, 10-15)
  • Gyradius Ratio 2 - 2nd Gyradius Ratio (r2 = PRG2 / PRG0) (also referred to as: r2) (See: Jian et al., 'A dimension map for molecular aggregates', J. Mol. Graphics. Model., 2015, 58, 10-15)

This node was developed by Vernalis Research. For feedback and more information, please contact knime@vernalis.com

Options

Molecule column
Select the input column

Calculated Properties

Principal Moment of Intertia (PMI)-Derived Properties
Select at least 1 property to calculate (see above for details)
Select All
Selects all properties
Clear
Deselects all properties, and selects only the 1st property in the list
Show All/Show 1st 15
Toggles the display of the options list between the first 15 options and all options

Input Ports

Icon
Input table

Output Ports

Icon
Input table with calculated properties appended

Views

This node has no views

Workflows

Links

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.