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  Physical Property Calculations in Molecular Modeling Pro

 

Bulk properties

  • molecular weight
  • molecular volume (van der Waal's volume) (MMP method, source code included with program, uses the calculation method and values of A. Bondi (J. Phys. Chem. 68:441, 1964))
  • surface area (MMP method, source code included with program)
  • density (MMP method)
  • molar volume (uses van Krevelen's additive method [Properties of Polymers, 3rd edition, Elsevier])
  • molecular length width and depth  (length along x, y and z axis and maximum length and width 90 degrees from the maximum length all calculated)

Log Kow (log P): three methods

  • fragment addition (after Hansch, Leo et.al.)
  • atom based (after Crippen, Ghose et.al.)
  • from CNDO charges

References

  • Fragment based:  Substituent Constants for Correlation Analysis in Chemistry and Biology by C. Hansch and A. Leo (1979), Wiley and Sons.
  • Atom based method: V.N. Viswanadhan, A.K. Ghose, G.R. Revankar and R.K. Robins, 1988, J. Chem. Inf. Comput. Sci., 29: 163-172.
  • The CNDO log P method: is a modified version of the article Environmental Toxicology and Risk Assessment - Third Volume, ASTM STP 1218, J.S. Hughes, G.R. Biddinger and E. Mones eds., Amercian Society for Testing and Materials, Philadelphia, 1995 (MMP uses CNDO charges instead of Gasteiger charges).

Solubility parameters

  • solubility parameters (dispersion, polarity and hydrogen bonding): 2 methods (van Krevelen, Properties of Polymers, 3rd edition, and an MMP unpublished method reproducing Hansen's values for solvents)
  • the solubility parameter (from 3-D parameters)
  • water solubility (G. Klopman, S. Wang and D.M. Balthasar, J. Chem. Inf. Comput. Sci. 32:474-482 (1992))
  • HLB (hydrophilic-lipophilic balance) (MMP unpublished method)
  • % hydrophilic surface area (MMP unpublished method)
  • hydrophilic surface area (MMP unpublished method)
  • mean water of hydration  (McGowan, Tenside Surfactants 27: 229-230 (1990))

Dipole moment and partial charges

  • modified DelRe method
  • Gasteiger and Marsili PEOE
  • No et.al. MPEOE
  • Huckel molecular orbital theory
  • Extended Huckel
  • CNDO (semiempirical quantum method)
  • comes with MOPAC for WINDOWS 95 (requires WINDOWS 95)

References:

  • Del Re method: G. Del Re, J. Chem. Soc. 4031 (1958); Poland and Scheraga, Biochemistry 6: 3791 (1967); Coefficients modified in MMP to take into account pi contributions - values in the file delre.txt, which can be modified by the user.
  • PEOE method: J. Gasteiger and M. Marsili, Tetrahedron 36:3219 (1980).
  • MPEOE (DQP) method: K.T. No, J.A. Grant and H.A. Scheraga, J. Phys. Chem. 94:4732 (1990) and K.T. No, J.A. Grant, M.S. Jhou and H.A. Scheraga, J. Phys. Chem. 94: 4740 (1990); J.M. Park, K.T. No, M.S. Jhou and H.A. Scheraga, J. Comp. Chem. 14:1482 (1993).

Connectivity indices

  • connectivity indices 0-4 (after Randic, Kier, Hall)
  • valence indices 0-4
  • Kier's kappa shape index 2
  • Wiener's number
  • difference indices

References:

L.B. Kier, L.H. Hall, W.J. Murray and M. Randic, J. Pharmaceutical Sci. 64: 1971-1974 (1975); W.J. Murray and L.B. Kier, J. Med. Chem. 19: 573-578 (1976); L.B. Kier, Quant. Struct.-Act. Relat. 4: 109-116 (1985); L.B. Kier and L.H. Hall, Molecular Connectivity in Chemistry and Drug Res., Academic, New York, 1976. The algorithm used to calculate this is included in a sample program that comes with MMP.

Polymer properties (after van Krevelen)

  • solubility parameter
  • glass transition temperature
  • melt transition temperature
  • molar water content at several different relative humidities
  • number of backbone atoms (Z)
  • Note: the program has a 4000 atom limit, but most polymer properties can be calculated from smaller polymer fragments

Reference: (D.W. van Krevelen, Properties of Polymers, 3rd edition, 1990, Elsevier)

Surfactant properties  

  • surface tension in 1% aqueous suspension
  • EO and PO content
  • % EO, % PO
  • likely form of micelles
  • HLB (hydrophilic lipophilic balance)
  • hydrophobic volume
  • hydrophobic maximum length
  • area of slice through hydrophilic region
  • Uses MMP unpublished methods for these properties

Sterimol parameters

  • L1, B1 and B5 (after Verloop)
  • B2, B3, B4, B6, B7, B8 calculated in a slightly different, consistent manner
  • Reference: A. Verloop, W. Hoogenstraaten and J. Tipker (1976). In Drug Design (ed. J. Ariens), pp. 165-207.  Values will not be reproduced exactly, since the MMP calculates directly from the distances drawn on the screen.

Hammett sigma substituent parameter

  • sigma para, sigma meta
  • sigma induction (SIND)
  • sigma star
  • uses an unpublished MMP method to estimate these values

Joback and Reid thermodynamics

  • Normal boiling point
  • Normal freezing point (least accurate calculation)
  • Critical temperature
  • Critical pressure
  • Critical volume
  • Enthalpy of formation
  • Gibbs energy of formation, ideal gas, unit fugacity, at 298 K
  • Enthalpy of vaporization, at boiling point
  • Enthalpy of fusion
  • Liquid viscosity at varied temperature
  • Heat capacity, ideal gas at varied temperature

Reference: (K.G. Joback and R.C. Reid, Chem. Eng. Comm. 57:233-243 (1987)

Other properties

  • boiling point  (after Handbook of Physical Properties Estimation)
  • vapor pressure (for liquids there are two methods)
  • molar refractivity (MR)
  • parachor
  • heat of vaporization
  • mass percent
  • moments of inertia (MMP unpublished method)
  • hydrogen bond acceptor and donor sums (MMP unpublished method)
  • viscosity  (D. van Velzen, R.L. Cardozo and H. Lnagenkamp, Ind. Eng. Chem. Fundam. 11:20 (1972))
  • surface tension of pure liquids 
  • entropy of boiling (Myrdal and Yalkowsky, 1997)
  • heat capacity change on boiling (Myrdal and Yalkowsky, 1997)
  • SMILES notation calculated from structures

Reference:  Handbook of Chemical Property Estimation Methods, W.J. Lyman, W.F. Reed, D.H. Rosenblatt, McGraw Hill (1982).  Some modifications have been made to these methods to reproduce literature values of boiling point and vapor pressure.  The MR, parachor, surface tension and heat of vaporization methods are also from this reference.  The second vapor pressure method (liquids only) is   P. Myrdal, S. Yalkowsky,  Ind. Eng. Chem. Res. 36: 2494-99 (1997) and handles varied temperatures."

Numerous other properties are calculated by CNDO and MOPAC 6.0

  • heat of formation, ionization potential, bonding energy, HOMO, LUMO, etc.
  • MOPAC 6.0 requires WINDOWS 95 or better.

Data base creation

  • ASCII text files of the physical properties can be made from the program. Just pick the properties and the name of the data base and the program will save the properties and structure of any molecule you have drawn.
  • Automated creation of data bases of physical properties of whole directories of Molfiles or MACROMODEL files can be done with a few mouse clicks.
  • Automated creation of QSAR data bases from a single substructure, complete with literature values of pi, MR, sigma, and sterimol parameters can be done in a few minutes.
  • Data bases can be read with any program capable of reading in a comma separated value text field, including Microsoft Excel and Molecular Analysis Pro
  • With Molecular Analysis Pro MMP and PP!P are a complete QSAR/QSPR package.

3-D drawing program with geometry minimization

  • comes with a complete 3-D drawing and viewing capability
  • geometry minimization with standard and quick MM2, two MOLY minimization methods (steepest descent and simplex), conformational analysis (rigid rotor), and MOPAC (MNDO, PM3, AM1)

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