Journal Articles

Polymer Property Prediction in MOE

P. Moser
Chemical Computing Group Inc.

Introduction  | Polymer Properties  | Connectivity Indices  | Properties Calculated in MOE  | SVL Functions  | Future directions



The 1997.09 release of MOE includes the new polymer property predictions. The polymer utilities a predictions panel which calculates and displays over 50 polymer properties. A polymerize function is available to easily create MOE polymers from a given monomer repeat unit. Methods for creating report files containing the output of the polymer calculations are provided as well as a utility for performing the property predictions on a database of polymers. A selection function allowing the user to visually inspect the backbone of the polymer repeat unit is also provided.

MOE Polymer Properties

The ability to predict polymer properties computationally is an important tool, enabling the research chemist to eliminate certain polymer structures prior to the costly process of synthesizing the polymer. In the past the main method of predicting the polymer properties was to break down the polymer into substituent groups and to use look up tables to determine the experimental values of these groups and then to add the partial results together. This of course required that the experimental values were available. A fairly new technique is under investigation by Jozef Bicerano in his monologue "Prediction of Polymer Properties", Marcel Dekker Inc., 1996. This method utilizes the graph theoretical properties, the connectivity indices, of the polymer's repeat unit. Since all the properties are based on the graph of the polymer, the properties can be predicted for any polymer entered into MOE with no need for any database to be maintained for look up and no threat that the polymers substituent group properties will not be available. The polymer properties in MOE are all calculated using the techniques found in Bicerno's book.

MOE defines a polymer as a repeat unit contained within a single residue, flanked on either side by identical copies of the monomer with bonds attaching the residues at the repeat unit endcaps. MOE provides the Polymerize[] function to perform the copy operation and the bonding between the residues. The user is prompted for the endcap atoms or, if running in MOEBatch, the atoms may be given as atom keys.

The polymer predictions panel is simple to use. On opening, the panel displays an empty list. When the Predict button is pressed, the polymer properties are calculated for all polymers currently within the MOE system and the results are displayed in the list. The list shows the scalar properties for the polymer displayed in the Polymer option menu.

The Plot option menu shows a list of available plots. When the Plot button is pressed the property selected is plotted for all the polymers in the system. This gives the user a way to visually compare the property between polymers.

The output of the predictions can be sent to a file and stored for further reference. A text field is supplied for the file name, however, if no file name is given then the output is sent to the CLI.

The SVL command MOE_Polymer_MDB[] allows the chemist to calculate all the properties listed in the predictions panel on an entire database of polymers. For each polymer in a given database, the polymer properties are calculated and the results are entered in a database field whose names matches the Tag in the output vector. The results can then be plotted using the database plot facility and polymer entries may be selected based on output values within the plot area.

Connectivity Indices

The connectivity indices used in the property predictions are derived from the hydrogen-suppressed graph of the polymer repeat unit. Each atom is represented by a vertex in the graph, while the bonds becomes edges. The connectivity indices are defined as follows:
    Chi0 = sum over all vertices of (1/sqrt Delta)
    ChiV0 = sum over all vertices of (1/sqrt DeltaV)
    Chi1 = sum over all edges of (1/sqrt Beta)
    ChiV1 = sum over all edges of (1/sqrt BetaV)


    Delta = # heavy neighbors
    DeltaV = (Zv - NH)/(Z-Zv-1)
    Betaij = Deltai * Deltaj
    BetaVij = DeltaVi * DeltaVj
  • Zv = number of valence electrons of an atom
  • NH = number of hydrogens bonded to the atom
  • Z = the atomic number
Exceptions are defined by the following table:

Atom Hyb Nh Delta DeltaV   Atom Hyb Nh Delta DeltaV
C sp3 3 1 1   O sp3 1 1 5
    2 2 2       0 2 6
    1 3 3     sp2 0 1 6
    0 4 4   F --- 0 1 7
  sp2 2 1 2            
    1 2 3       0 4
    0 3 4   P sp3 2 1
  sp 1 1 3       1 2
    0 2 4       0 3
N sp3 2 1 3   S sp3 1 1
    1 2 4       0 2
    0 3 5       0 4
  sp2 1 1 4   Se sp3 0 2
    0 2 5   Cl --- 0 1
  sp 0 1 5   Br --- 0 1 7/27
    0 3 6   I --- 0 1 7/47

The exceptions outlined in the above table are built in to the MOE prediction routines. In general, a polymer property is predicted through a formula that uses some of the Chi values with additional correction indices added in. A common correction term is one that involves simply the number of atoms of a certain element type. For more information on the correction terms used for each property, we refer you to Bicerno's book, which explains in detail each term used in the prediction formulas.

Polymer Properties Calculated in MOE

MOE currently predicts over 50 polymer properties. They are divided into two groups, scalar properties and plottable properties. The scalar property results are displayed in the polymer panel while the plottable properties are listed in an option menu at the top of the panel and shown graphically in the plot window. Since the polymer panel can predict the properties for multiple polymers, the plot window can be used to visually compare the results between the polymers. The following polymer properties are currently calculated in MOE:

M Molecular Weight of Repeat Unit g/mol
Me Entaglement Molecular Weight g/mol
lm Length of Extended Repeat Unit A
V298 Amorphous Molar Volume cc/mol
Vvdw Van der Waals Volume cc/mol
p298 Amorphous Density g/cc
Ecoh1 Cohesive energy (Fedors) J/mol
Ecoh2 Cohesive energy (van Krevelen) J/mol
sol_Ecoh1 Solubility Parameter (Fedors) (J/cc)**0.5
sol_Ecoh2 Solubility Parameter (van Krevelen) (J/cc)**0.5
Tg Glass Transition Temperature K
a298 Volumetric thermal expansion 10**-6../TD>
C298 Heat Capacity J/molK
DeltaCpTg Heat Capacity Jump at Tg J/molK
g298_Ecoh1 Surface Tension (Fedors) dyn/cm
g298_Ecoh2 Surface Tension (van Krevelen) dyn/cm
g298 Surface Tension (molar parachor) dyn/cm
n298 Refractive Index -
RLL Molar Refraction cc/mol
dipole Effective Dipole Moment debyes
PLL Molar Polarization cc/mole
eps298 Dielectric Constant -
vr298 Volume Resistivity (log10) ohm cm
mag Magnetic Susceptibility 1e-6 ../TD>
sigma Steric Hindrance Parameter -
Cinf Characteristic Ratio -
viscosity Intrinsic Viscosity (molar stiffness) -
Mcr Critical Molecular Weight g/mol
Eact Activation Energy for Viscous Flow J/mol
l298 Thermal Conductivity J/Kms
pO2 Permeability to O2 Dow Units
pN2 Permeability to N2 Dow Units
pCO2 Permeability to CO2 Dow Units
Eact_d Activation Energy of Decomposition kJ/mol
T0_d Temperature of Initial Decomposition K
T_d Temperature of Half Decomposition K
Tmax_d Temperature of Maximum Decomposition K
Y_d Molar Thermal Decomposition Function kgK/mol
Fd Dispersion Component of Molar Attraction -

The following values are plots as a function of temperature. The temperature range calculated is 0-500K for all properties.

V(T) Molar Volume cc/mol
p(T) Amorphous Density g/cc
C(T) Heat Capacity J/molK
g(T) Surface Tension dyn/cm
n(T) Refractive Index -
B(T) Bulk Modulus MPa
v(T) Poisson's Ratio -
E(T) Young's Modulus MPa
G(T) Shear Modulus MPa
F(T) Brittle Fracture Stress Mpa
Y(T) Shear Yield Stress Mpa
l(T) Thermal Conductivity J/Kms

SVL Functions

MOE provides several SVL functions enabling the user to further take advantage of the new polymer facilities. These functions can be invoked through the menu options, at the command line, or from within SVL programs.
Polymerize []
This function is located in the main Edit menu. Input: The chain to be polymerized must have a single residue. The residue is copied twice and attached via the endcaps. Endcaps are prompted for from the user.

MOE_Polymer []
Accessible through the main Compute menu item 'Polymer Properties...', this function brings up the polymer predictions panel. If the panel is already up, then calling this function will deiconify and raise the polymer panel so that it is visible.

MOE_Polymer_MDB []
For each polymer in a given database, calculate all the polymer properties and enter the result in a database field. The field names are those given in the above property table Tag column.

MOE_Polymer_Selectbackbone []
Called with no arguments, this function will select the atoms in the repeat unit that are part of the backbone for each correct polymer currently in MOE.

Future directions

Additional properties are being studied for inclusion into the prediction utility. As well, Chemical Computing Group plans to expand the polymer facilities available in MOE. Some of the features under consideration the ability to:
  • enter a personalized Tg, Glass Transition Temperature, for any specific polymer to be used in the calculations.
  • give a temperature range for each property that is graphed as a function of temperature.
  • handle tacticity of polymers.