Substructure Thermodynamic Corrections

Substructure Corrections with Thermodynamic data

For a substructure has thermodynamic associated with it, the input comes in a group (3-4 lines) with the following information:

The structure, one or two lines (line 1 and 1a: JThergasStructureData)
The Benson information line 2:
Atomic Makeup (sometimes not used)

This information is used in connection with introducing the following corrections:

Benson rules: In this case the structure is given as a benson rule. Here the information is given in three lines
Cyclic Correction: here the substructure is a general cyclic structure. Here the information is given in four lines.
Steric Corrections: Here the structure is a general one. The information is given in four lines.
Molecules: This is the thermodynamic information for a specific molecule (meaning it does not need to be calculated)

The decision of whether it is 3 or 4 lines is by convention, but mainly decided by whether the substructures definition can be long.

The substructure corrections have four lines:

1  60 1.cyclopropane ring                               1 0.0 1.0     1 1.0j73

l  cR2(#1)/cR2/cR2/1

1  60 2  1  27.600 1  32.100 1 -3.05 -2.53 -2.10 -1.90 -1.77 -1.62 -1.52 0 j73

1  60 3  0 0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0j7

and the benson rules, for example, have three lines:

 1   1 1 c-(h)/3-(c)                                     0 0.0 3.0     1 1.0j73

 1   1 2  1 -10.098 1  30.423 1  6.15  7.84  9.40 10.79 13.02 14.77 17.58 0 j73

 1   1 3  0 0  0  1  0  0  0  0  0  3  0  0  0  0  0  0  0  0  0  0  0  0  0j73

Parsing lines 1 and 1a by JThergasStructureData

This parses line 1, supplemented with line 1a of the thermo block. These two lines are parsed by the

jThergas.data.structure.JThergasStructureData

data structure. Parsing the lines produces the following information:

table number
group number
name of the structure
nancy linear form;
INDIC
optical symmetry
internal symmetry
external symmetry
date as string
formula given (true or false)
formula
group

           1         2         3         4         5         6         7         8 0123456789012345678901234567890123456789012345678901234567890123456789012345678901

  1  60 1.cyclopropane ring                               1 0.0 1.0     1 1.0j73

_TTGGGGBB_NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNIOOOOIIII      EEEEDDD

l  cR2(#1)/cR2/cR2/1

_BBSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS

Line 1:

(0,0) Blank

(1,2) The table number

(3,6) The group number

(7,8) if a group (from boolean):

If group '1.' then (10,57) the Nancy linear form
If not group '1.' (10,27) The Nancy linear form (28,57) The structure name

(58,58) INDICS

(59,62) optical symmetry

(62,66) internal symmetry

(73,76) external symmetry

(77,79) date

Line 1a:

(0,0) Blank or l

(1,2)

(3,-)  Structure name

Parsing 2nd line by JThergasThermoData

jThergas.data.thermo.JThergasThermoData

tableNumber
groupNumber
standardEnthalpy
enthalpyReference
standardEntropy
entropyReference
cpValues
heatCapacityReference1
heatCapacityReference2

          1         2         3         4         5         6         7         8 0123456789012345678901234567890123456789012345678901234567890123456789012345678901

  1  60 2  1  27.600 1  32.100 1 -3.05 -2.53 -2.10 -1.90 -1.77 -1.62 -1.52 0 j73

_TTGGGG22_RREthalpy-RREntropy-RR 000000111111222222333333444444555555666666RR

(0,0) Blank

(1,2) tableNumber

(3,6) groupNumber

(7,8) 2

 (9,9)

 (10,11) enthalpyReference

(12,19) standardEnthalpy

(20,21) entropyStandard

(22,29) standardEntropy

(30,31) heatCapacityReference

(33,38) cpValues[0] (300)

(39,44) cpValues[1] (400)

(45,50) cpValues[2] (500)

(51,56) cpValues[3] (600)

(57,62) cpValues[4] (800)

(63,68) cpValues[5] (1000)

(69,74) cpValues[6] (1500)

Parsing 3r line with JThergasAtomicStructure

jThergas.data.structure.JThergasAtomicStructure

tableNumber
groupNumber
numberOfAtomsA1
numberOfAtoms
dateString

(0,2) table number

(3,6) group number

(7,8) line number

(11,12) number of atoms

(13,15) Br   35

(16,18) C    6

(19,21) Cd   48

(22,24) Cl   17

(25,27) Ch   0

(28,30) F    9

(31,33) Ge   32

(34,36) H    1

(37,39) Hg   80

(40,42) I    53

(43,45) N    7

(46,48) O    8

(49,51) P    15

(52,54) Pb   82

(55,57) S    16

(58,60) Si   14

(61,63) Sn   50

(64,66) Ti   22

(67,69) V    23

(70,72)Zn    30

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