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AdditionalCompounds
Note that only a handful of compounds are defined within the tlvmie-simulation program. Additional compounds can be added in the following manner:
- A row must be added to
tlvmie-simulation/resources/compound_lookup.csv, with all fields populated in the manner of the other compounds. Fields should be tab-delimited. Note that commas are illegal characters in the tlvmie-simulation script, so compounds whose names contain commas should be replaced with hyphens when possible. For example,2,2,4,4,6,8,8-heptamethylnonaneis named2-2-4-4-6-8-8-heptamethylnonane. The columns in this csv are as follows:- compound: Compound name
- 298Kvol1000: unused--can be left as null
- DIPPRvisc: unused--can be left as null
- Dens: unused--can be left as null
- NumAtoms: Number of atoms in compound
- UA: Number of atoms in United Atom representation of compound
- dens_A: fitting parameter 'A' in DIPPR's equation 105 for liquid density. Found in DIADEM
- dens_B: fitting parameter 'B' in DIPPR's equation 105 for liquid density. Found in DIADEM
- dens_C: fitting parameter 'C' in DIPPR's equation 105 for liquid density. Found in DIADEM
- dens_D: fitting parameter 'D' in DIPPR's equation 105 for liquid density. Found in DIADEM
- visc_A: fitting parameter 'A' in DIPPR's equation 101 for liquid viscosity. Found in DIADEM
- visc_B: fitting parameter 'B' in DIPPR's equation 101 for liquid viscosity. Found in DIADEM
- visc_C: fitting parameter 'C' in DIPPR's equation 101 for liquid viscosity. Found in DIADEM
- visc_D: fitting parameter 'D' in DIPPR's equation 101 for liquid viscosity. Found in DIADEM
- visc_E: fitting parameter 'E' in DIPPR's equation 101 for liquid viscosity. Found in DIADEM
- T_m: Melting point of the compound
- T_c: Critical temperature of the compound
- potoff: This field is mislabeled. Should read "S/L". Enter 'S' if the longest alkyl carbon chain length is 4 or less carbons long. Enter 'L' if 5 or longer. This field is specifically for alkyl branching per 10.1016/j.fluid.2022.113681. E.g.,
- n-pentane: 'L'
- n-butane: 'S'
- n-butylbenzene: 'S'
- iso-butylbenzene: 'S'
- sec-butylbenzene: 'S'
- 1,3,5-tri-iso-propylbenzene: 'S'
- 2,2,3-trimethylbutane: 'S'
- 3-methyl-3-ethylpentane: 'L'
- CAS: CAS number for the compound
- shorthand: shorthand name for the compound. Must not contain any special characters. E.g., 2,4-dimethylpentane -> 24dimethylpentane
- T_b: Normal boiling point of the compound
- Also, a folder containing the compound name must be placed in
tlvmie-simulation/resources/block_compounds. The folder structure should be as follows:
tlvmie-simulation/resources/block_compounds/:
COMPOUNDNAME---|
|-moltemplate_files---|
| |---COMPOUNDNAME_FORCEFIELD.lt
|
|
|-packmol_files-------|
|---CASNUM_COMPOUNDNAME_FFTYPE.xyz
Example:
tlvmie-simulation/resources/block_compounds/:
2-2-4-trimethylpentane---|
|-moltemplate_files---|
| |---2-2-4-trimethylpentane_TLVMie.lt
| |---2-2-4-trimethylpentane_MiPPE.lt
| |---2-2-4-trimethylpentane_TraPPEUA.lt
| |---2-2-4-trimethylpentane_OPLSAA.lt
|
|
|-packmol_files-------|
|---540-84-1_2-2-4-trimethylpentane_UA.xyz
|---540-84-1_2-2-4-trimethylpentane_AA.xyz
A description of the COMPOUNDNAME_FORCEFIELD.lt and CASNUM_COMPOUNDNAME_FFTYPE.xyz files follows below.
###################################################
######## 2-2-4-trimethylpentane_TLVMie.lt #########
###################################################
import "TLVMie.lt"
224trimethylpentane inherits TLVMie {
#
# CH3 CH3 (4) (7)
# | | | |
# CH3 - CH0 CH1 (6) - (1) (3)
# / \ / \ / \ / \
# CH3 CH2 CH3 (5) (2) (8)
#
# atomID molID atomType charge X Y Z
write('Data Atoms') {
$atom:C1 $mol @atom:CH0 0.00 -1.1545 -0.0936 0.0108 # Alkane -CH0-
$atom:C2 $mol @atom:CH2 0.00 0.2112 -0.7723 0.3209 # Alkane -CH2-
$atom:C3 $mol @atom:CH1 0.00 1.4706 -0.1336 -0.3107 # Alkane -CH1-
$atom:C4 $mol @atom:CH3 0.00 -2.3309 -1.074 0.109 # Alkane -CH3
$atom:C5 $mol @atom:CH3 0.00 -1.141 0.5409 -1.392 # Alkane -CH3
$atom:C6 $mol @atom:CH3 0.00 -1.3731 1.0313 1.0438 # Alkane -CH3
$atom:C7 $mol @atom:CH3 0.00 1.5644 1.3445 0.0845 # Alkane -CH3
$atom:C8 $mol @atom:CH3 0.00 2.7535 -0.8433 0.1338 # Alkane -CH3
}
# Charges will be assigned by OPLSAA, so we leave them 0.0 here.
#
# (The "." in "$mol:." refers to this molecule-object's molecule-ID number.
# The "." simply means this molecule is not a part of a larger molecule.)
write('Data Bond List') {
$bond:C12 $atom:C1 $atom:C2
$bond:C14 $atom:C1 $atom:C4
$bond:C15 $atom:C1 $atom:C5
$bond:C16 $atom:C1 $atom:C6
$bond:C23 $atom:C2 $atom:C3
$bond:C37 $atom:C3 $atom:C7
$bond:C38 $atom:C3 $atom:C8
}
} # 224trimethylpentane
###################################################
##### End of 2-2-4-trimethylpentane_TLVMie.lt #####
###################################################
The COMPOUNDNAME_FORCEFIELD.lt file contains charges and atom coordinates for the united-atom groups contained in the molecule. These are contained in the write('Data Atoms') section.
Columns in this section are:
- atomID - these are arbitrary, but typically just C1, C2, ..., etc.
- molID - Leave as
$molfor all but single-molecule system - atomType - Specifies the group type as defined in
tlvmie-simulation/software/moltemplate/moltemplate/force_fields/FORCEFIELD.lt - charge - Charge associated with the group
- X - x coordinates of the pseudoatom/group
- Y - y coordinates of the pseudoatom/group
- Z - z coordinates of the pseudoatom/group
The X, Y Z coordinates are pulled from NIST's computed 3d SD files (*.sdf) NIST webbook, 2,2,4-trimethylpentane (click the "3d SD file" link).
The write('Data Bond List') section contains the bonds present in the molecule. Columns in this table are:
- bondID - Can be a name, this work just uses
$bond:CXY - bondedatom1 - The atomID of the first atom in this bond (
$atom:CX) - bondedatom2 - The atomID of the second atom in this bond (
$atom:CY)
The import "TLVMie.lt" line at the top of the file references the force field definition file present at tlvmie-simulation/software/moltemplate/moltemplate/force_fields/TLVMie.lt. References to different force fields would require adjusting this line.
The same X, Y, Z coordinates stored in the COMPOUNDNAME_FORCEFIELD.lt file are stored in the CASNUM_COMPOUNDNAME_FFTYPE.xyz file, which has the following structure:
######################################################### ######## 540-84-1_2-2-4-trimethylpentane_UA.xyz ######### ######################################################### 8 C -1.15450 -0.09360 0.01080 C 0.21120 -0.77230 0.32090 C 1.47060 -0.13360 -0.31070 C -2.33090 -1.07400 0.10900 C -1.14100 0.54090 -1.39200 C -1.37310 1.03130 1.04380 C 1.56440 1.34450 0.08450 C 2.75350 -0.84330 0.13380 ######################################################### ##### End of 540-84-1_2-2-4-trimethylpentane_UA.xyz ##### #########################################################
The numeral 8 represents the number of atoms (united-atom) in the molecule. For 2,2,4-trimethylpentane, this is 8 (8 carbon atoms). For something like n-hexane, it would be 6, and for 1-hexanol with explicit functional group hydrogen and oxygen, 8 (6 carbons, 1 alcohol O, 1 alcohol H).
The all-atom equivalent is shown below for reference (this would be used with all-atom force fields, like OPLSAA). Note that the number of total atoms is 26 here, since the alkyl hydrogens are represented explicitly in all-atom force fields.:
######################################################### ######## 540-84-1_2-2-4-trimethylpentane_AA.xyz ######### ######################################################### 26 C -1.15450 -0.09360 0.01080 C 0.21120 -0.77230 0.32090 C 1.47060 -0.13360 -0.31070 C -2.33090 -1.07400 0.10900 C -1.14100 0.54090 -1.39200 C -1.37310 1.03130 1.04380 C 1.56440 1.34450 0.08450 C 2.75350 -0.84330 0.13380 H 0.16730 -1.80540 -0.05210 H 0.34480 -0.86610 1.40690 H 1.42090 -0.20770 -1.40310 H -2.23090 -1.87970 -0.62680 H -3.29050 -0.57650 -0.07090 H -2.37380 -1.53430 1.10240 H -2.15650 0.85940 -1.66260 H -0.52880 1.42830 -1.52060 H -0.84000 -0.19540 -2.14650 H -0.73090 1.90150 0.91800 H -2.39900 1.41470 0.97090 H -1.24850 0.66110 2.06790 H 1.47020 1.47180 1.16870 H 2.55990 1.72590 -0.17880 H 0.88060 2.02090 -0.41810 H 2.89180 -0.77310 1.21810 H 3.63270 -0.40610 -0.35120 H 2.71760 -1.90440 -0.13450 ######################################################### ##### End of 540-84-1_2-2-4-trimethylpentane_AA.xyz ##### #########################################################