• The Molecular Polarizability
  
  A general formula, based on MM3 bond stretching force parameters as well as bond dipole moment parameters, is used to compute bond polarizabilities. The molecular polarizability is then calculated using the bond polarizability contributions and an additive model. No new parameters for individual bond polarizabilities are required.
  
  Reference:
  
  Ma, B; Lii, J.-H.; Allinger, N. L. "Molecular Polarizabilities and Induced Dipole Moments in Molecular Mechanics", in preparation.
  
  
• Induced Dipole Moments
  
  The pair-interaction approximation, using the parameterized bond "permanent" dipole moments as well as the bond polarizabilities, is used to calculate dipole-induced dipoles and the total molecular dipole moment. The pair-interaction approach was chosen for use in the program since it involves much less computation than the traditional many-body-interaction approach.
  
  Reference:
  
  Ma, B; Lii, J.-H.; Allinger, N. L. "Molecular Polarizabilities and Induced Dipole Moments in Molecular Mechanics", in preparation.
  
  Note:
  
  
  • The MM3(2000) program also calculates the dipole/induced dipole energy term and prints it. However, the feature is still under the development, and no use is made of this number.
    
  • The induced dipole moment will not be calculated if any "permanent" bond moment in the molecule had not been parameterized.
    
  
  
• Inclusion of Electron Correlation in the Conjugated System
  
  Electron correlation at the Moller-Plesset second-order level (MP2) was incorporated into the Pi-system portion of MM3 calculations. Correlation always lowered the energies of the delocalized conformation more than it did that of the localized conformation, such that often the former was found to be more stable after correlation energy was included in the calculation. When a delocalized structure was not at a stationary point on the MM3 energy surface, such comparison could not be made. This eliminates a major source of errors in structures of conjugated systems in MM3 (for example, in [18]annulene). The error stems from the Hartree-Fock approximation, not from the molecular mechanics approximations.
  
  Reference:
  
  Tai, J. C.; Allinger, N. L. "Effect of Inclusion of Electron Correlation in MM3 Studies of Cyclic Conjugated Compounds", J. Comput. Chem., 19, 475, 1998.
  
  Note:
  
  • To include MP2 type electron correlation in the MM3 calculation, the users need to specify METHOD "2" (instead of METHOD "1") Pi-system calculation in their MM3 input file - CPD.MM3 (column 61 of the "Name" card). Please see "MM3 Manual Update" section at the end of this release note.
    
    METHOD 0: Non-conjugated calculation.
    METHOD 1: Conjugated Pi-system VESCF calculation.
    METHOD 2: Conjugated Pi-system MP2 calculation.
    
    
  • The maximum number of Pi-atoms allowed in the MP2 calculation is limited to 50 Pi- atoms due to the memory and CPU time consideration.
    
  
  
  

  Improvements and Corrections

  
  
  
• The default maximum number of internal coordinates to be monitored in the Molecular Dynamic Simulation is increased from 50 to 100. This change will allow the user to put more internal coordinates in the list. A large value (up to 100) may be read in if desired as previously.
  
  
• For the user's convenience, the MM3(2000) Molecular Dynamic program now will generate the trajectory history file (fort.22) for the molecular dynamic analyzer program "Re_View" created by Dr. Jeffery J. Gosper. The Re_View is a freeware program for Window95/98/NT. It can be downloaded freely from the internet by the individual user. Its websites are
  
  http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm
  or,
  http://www.softshell.com/Free/REVIEW/Re_View.html
  
  
• The bug which caused molecular tumbling during the Molecular Dynamic Simulation has been fixed in the current version of the program.
  
  
• Other minor bugs have also been fixed. Many thanks to those who send us the bug reports.
  
  
  

  New Parameters in MM3(2000)
  These may be read in to earlier versions of the program
  

  
  1. Organogermanes ---- Chen, K.; Allinger, N. L. "Molecular Mechanics (MM3) Study of Organogermanes", J. Phys. Org. Chem., in press, 1999.
  
  2. Phosphates --- Stewart, E. L.; Nevins, N.; Bowen, J. P.; Allinger, N. L. "Molecular Mechanics (MM3) Calculations on Some Oxygen-Containing Phosphorous (Coordination IV) Compounds", J. Org. Chem., in press, 1999.
  
  3. Fluorinated Hydrocarbons --- Chen, K.; Walker, G. A.; Allinger, N. L. "A Molecular Mechanics (MM3) Study of Fluorinated Hydrocarbons", J. Mol. Struct. (THEOCHEM), in press, 1999.
  
  4. Oxocarbenium Ions --- Liang, G.; Sorensen, J.; Whitmire, D.; Bowen, J. P. "Molecular Mechanics (MM3) Paramerization for Oxocarbenium Ions", J. Comput. Chem., 1999.
  
  5. Ammonium Ion Related Parameters Correction --- Sorensen, J. B.; Lewin, A. H.; Bowen, J.P. "An Ab Initio Study of the Electrostatics of Ammonium Ions: Application to Molecular Mechanics (MM3)", submitted to J. Comput. Chem., 1999.
  
                   MM3(96) MM3(2000)
  Stretching Parameters:
  Ks / lo / Moment Ks / lo / Moment
  1-39 4.2741 / 1.5031 / -0.5265 4.2741 / 1.5110 / 3.335
  39-48 6.1402 / 1.0283 / -1.9219 6.1402 / 1.0530 / -1.300
  
  Electronegativity Correction:
  lo correction lo correction
  1-1 1 39 -0.0110 -0.0037
  1-5 1 39 -0.0128 0.0010
  
  Torsional Parameters:
                   V1 / V2 / V3 V1 / V2 / V3
  8-1-1-39 7.582 / -4.588 / 1.600 1.000 / -3.500 / 3.000
  39-1-1-39 -10.382 / -3.021 / 0.637 4.800 / -3.800 / 0.637
  
  
  6. The O-C-O-H (type 6-1-6-21) Torsion Parameters Update:
                    MM3(96) MM3(2000)
  Torsional Parameters:
                   V1 / V2 / V3      V1 / V2 / V3
  6-1-6-21  0.000/0.000/0.000    -1.832/-2.208/0.547
  
  
  7. Zwitterions --- Kirschner, K. N.; Lewin, A. H.; Bowen, J. P. "Molecular Mechanics (MM3) Force Field Development of Zwitterion Parameters", in preparation.
  
  8. Oximes --- Arias, L. A.; Lii, J.-H.; Bowen, J. P. "Ab initio and Molecular Mechanics (MM3) for Oximes and some of their derivatives", in preparation.
  
  

  MM3 Manual Update

  
  Molecular Structure Data File: CPD.MM3
  1 Name card  (6A10, I1, I4, I2, I1, 2I2, I3, F5.0)
  
  1-60  ID                   Alphanumeric identification
     61  METHOD  0  All molecules except conjugated Pi-system
                               1  Conjugated Pi-system VESCF calculation
                               2  Conjugated Pi-system MP2 calculation
                                   .......
                                   .......
                                   .......