Chapter 34. Use of Partial Charge Sparkles

Chapter 34. Use of Partial Charge Sparkles
	Part II. AMPAC™ 10 Examples

Table of Contents

Input File (general/gen_sparkles_symmetry.dat):
Ouput File (general/gen_sparkles_symmetry.out):

As mentioned in Chapter 5, Presenting Input to the Program, sparkles may be defined with partial charges to simulate the electrostatic interaction between the molecular system and some surrounding environment such as a solvent, counterion, or active site. To illustrate this concept, gen_sparkles_symmetry.dat consists of a water molecule polarized by two oppositely charged sparkles in the following arrangement:

Figure 34.1. Water molecule polarized by two “sparkles.”

Input File (`general/gen_sparkles_symmetry.dat`):

  am1 rhf singlet t=1h truste symmetry grad bonds=all
WATER WITH TWO PARTIAL CHARGED SPARKLES
SPARKLES w/ PARTIAL CHARGES, Na and Cl, T W/ HOURS
 O              0.000000  0    0.000000  0    0.000000  0    0    0    0
 +              1.000000  0    0.000000  0    0.000000  0    1    0    0   0.50   
 H              1.000000  1  128.300000  1    0.000000  0    1    2    0
 H              1.000000  1  128.300000  1  180.000000  0    1    2    3
 -              2.000000  0  128.300000  0  180.000000  0    1    3    4  -0.50   
 0              0.000000  0    0.000000  0    0.000000  0    0    0    0
$$ symmetry - constraints   
  3, 1, 4,
  3, 2, 4, 5,
$$ end of extra data

	The “+” sparkle is assigned a charge of 0.50 in the rightmost column.
	The “-” sparkle is assigned a charge of -0.50 in the rightmost column.
	This is the extra input section marker for symmetry data. Note, that this marker can be shortened to “$$ symm”. Details of these markers are found in the section called “Extra Input Data”.

Ouput File (`general/gen_sparkles_symmetry.out`):

 Timestamp: 2011-08-31-12-44-50-0000001038-win64
 User Info: John Millam, Nahum, 
 *******************************************************************************
                         AM1 CALCULATION RESULTS
 *******************************************************************************
 *                             AMPAC Version 10.0.1
 *                                Presented by:
 *
 *                           Semichem, Inc.
 *                           www.semichem.com
 *
 *  AM1      - THE AM1 HAMILTONIAN TO BE USED
 *  RHF      - RESTRICTED HARTREE-FOCK CALCULATION
 *  TRUSTE   - MINIMIZE ENERGY USING TRUST REGION METHOD
 *  SYMMETRY - SYMMETRY CONDITIONS TO BE IMPOSED
 *  T=       - A TIME OF      3600 SECONDS REQUESTED
 *  BONDS=ALL- PRINT ALL ELEMENTS OF FINAL BOND-ORDER MATRIX
 *  GRADIENTS- ALL GRADIENTS TO BE PRINTED
 *  SINGLET  - IS THE REQUIRED SPIN MULTIPLICITY
 *******************************************************************************
 AM1 RHF SINGLET T=1H TRUSTE SYMMETRY GRAD BONDS=ALL
 WATER WITH TWO PARTIAL CHARGED SPARKLES
 SPARKLES w/ PARTIAL CHARGES, Na and Cl, T W/ HOURS
 THE SPARKLE No   2 ACCOUNTS FOR  1 TO THE CHARGE ON THE SYSTEM    
                    BUT HOLDS A CHARGE  0.50000
 THE SPARKLE No   5 ACCOUNTS FOR -1 TO THE CHARGE ON THE SYSTEM
                    BUT HOLDS A CHARGE -0.50000

     PARAMETER DEPENDENCE DATA
        REFERENCE ATOM      FUNCTION NO.    DEPENDENT ATOM(S)
            3                  1             4
            3                  2             4  5

            DESCRIPTIONS OF THE FUNCTIONS USED
   1      BOND LENGTH    IS SET EQUAL TO THE REFERENCE BOND LENGTH   
   2      BOND ANGLE     IS SET EQUAL TO THE REFERENCE BOND ANGLE    

    ATOM    CHEMICAL   BOND LENGTH    BOND ANGLE    TWIST ANGLE
   NUMBER   SYMBOL     (ANGSTROMS)     (DEGREES)     (DEGREES)
    (I)                   NA:I          NB:NA:I      NC:NB:NA:I     NA    NB    NC
      1     O 
      2     +          1.00000                                       1
      3     H          1.00000 *      128.30000 *                    1     2
      4     H          1.00000        128.30000     180.00000        1     2     3
      5     -          2.00000        128.30000     180.00000        1     3     4

   MOLECULAR POINT GROUP            SYMMETRY CRITERIA
            C2v                         0.10000000

          SINGLET STATE CALCULATION

          RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =       4

        **  REFERENCES TO PARAMETERS  **

 H  (AM1):  M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985).
 O  (AM1):  M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985).
 +  SPARKLE:  ALL METHODS.
 -  SPARKLE:  ALL METHODS.

          CARTESIAN COORDINATES
      ATOM            X               Y               Z
       1 O        0.00000000      0.00000000      0.00000000
       2 +        1.00000000      0.00000000      0.00000000
       3 H       -0.61977903      0.78477637      0.00000000
       4 H       -0.61977903     -0.78477637      0.00000000
       5 -        2.00000000      0.00000000      0.00000000

 STANDARD DEVIATION ON ENERGY   (KCAL)       0.00000055519
 STANDARD DEVIATION ON GRADIENT (KCAL/A,RD,RD)  0.00009841 0.00022004 0.00000000

 AM1 RHF SINGLET T=1H TRUSTE SYMMETRY GRAD BONDS=ALL
 WATER WITH TWO PARTIAL CHARGED SPARKLES
 SPARKLES w/ PARTIAL CHARGES, Na and Cl, T W/ HOURS

     GEOMETRY OPTIMIZED : ENERGY MINIMIZED
     SCF FIELD WAS ACHIEVED

                              AM1 CALCULATION
                                                            VERSION 10.0.1

                                                       Aug-31-2011
 
          FINAL HEAT OF FORMATION   =       122.807378 kcal       
                                    =       513.948877 kJ
          ELECTRONIC ENERGY         =      -505.418009 eV
          CORE-CORE REPULSION       =       164.749666 eV
          TOTAL ENERGY              =      -340.668343 eV
          GRADIENT NORM             =         0.004885 
          RMS GRADIENT NORM         =         0.003455 
          UNSTABLE MODE(S)          =         0 ( ESTIMATE  )
          IONIZATION POTENTIAL      =        13.937193 eV
          HOMO-LUMO GAP             =        17.170605 eV
          MOLECULAR WEIGHT          =        18.015200 
          MOLECULAR POINT GROUP     = C2v     0.100000
          NO. OF FILLED LEVELS      =         4 (OCC = 2)
          TOTAL NUMBER OF ORBITALS  =         6
          SCF CALCULATIONS          =         8
          COMPUTATION TIME          =         0.16     SECONDS

       FINAL GEOMETRY AND DERIVATIVES
   PARAMETER    ATOM     TYPE            VALUE       GRADIENT
      1          3 H     BOND            0.975724    -0.001064  kcal/angstrom
      2          3 H     ANGLE         129.185666     0.004768  kcal/radian  
 
    ATOM    CHEMICAL   BOND LENGTH    BOND ANGLE    TWIST ANGLE    
   NUMBER   SYMBOL     (ANGSTROMS)     (DEGREES)     (DEGREES)
    (I)                   NA:I          NB:NA:I      NC:NB:NA:I     NA    NB    NC
      1     O 
      2     +          1.00000                                       1
      3     H          0.97572 *      129.18567 *                    1     2
      4     H          0.97572        129.18567     180.00000        1     2     3
      5     -          2.00000        129.18567     180.00000        1     3     4

   MOLECULAR POINT GROUP            SYMMETRY CRITERIA
            C2v                         0.10000000

          RHF EIGENVALUES
    -37.66084    -19.27057    -16.84049    -13.93719      3.23341      4.81211

          NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS    
      ATOM            CHARGE        ATOM ELECTRON DENSITY
       1 O           -0.4643          6.4643
       2 +            0.5000          0.0000
       3 H            0.2321          0.7679
       4 H            0.2321          0.7679
       5 -           -0.5000          0.0000

 DIPOLE (DEBYE)   X         Y         Z       TOTAL
 POINT-CHG.    -3.776     0.000     0.000     3.776
 HYBRID        -0.752     0.000     0.000     0.752
 SUM           -4.528     0.000     0.000     4.528


          CARTESIAN COORDINATES
      ATOM            X               Y               Z
       1 O        0.00000000      0.00000000      0.00000000
       2 +        1.00000000      0.00000000      0.00000000
       3 H       -0.61649701      0.75628624      0.00000000
       4 H       -0.61649701     -0.75628624      0.00000000
       5 -        2.00000000      0.00000000      0.00000000


          ATOMIC ORBITAL ELECTRON POPULATIONS
      1.85966      1.37307      1.23154      2.00000      0.76786      0.76786

                    BOND ORDERS AND VALENCIES

                  1 O        2 +        3 H        4 H        5 - 
 -----------------------------------------------------------------
       1 O    1.892224
       2 +    0.000000   0.000000
       3 H    0.946112   0.000000   0.946113
       4 H    0.946112   0.000000   0.000000   0.946113
       5 -    0.000000   0.000000   0.000000   0.000000   0.000000
 
     ELAPSED WALL CLOCK TIME :      0.17 SECONDS
     FULL COMPUTATION TIME :      0.16 SECONDS

The contribution and charge information for the sparkles is presented here. Note that the total charge on the system is a function of the charge of the sparkles. Thus if two “+” sparkles (even a “+” sparkle could hold a negative partial charge) had been used instead, the total charge on the system would have been +2.

There is a large increase in the system’s energy due to the polarization by the sparkles. The normal AM1 heat of formation for water is -59.2 kcal/mol.

The geometry has been distorted by the presence of the sparkles. The HOH angle has increased to about 129° and the bonds are slightly longer than in regular water.

The effect of the sparkles can also be seen in the electron distribution on the atoms. A comparison of the atomic charges with and without sparkles is listed below. The near proximity of the +0.500 sparkle has the effect of concentrating more negative charge on the oxygen atom as expected. The hydrogens are thus slightly more positive.

Table 34.1. Effect of presence of sparkles

Method	Charge on O	Charge on H

Sparkles	-0.4643	0.2321
No Sparkles	-0.3827	0.1913


Chapter 33. Polarizability (KPOLAR, APOLAR)		Part III. AMPAC™ 10 User Reference