Professional Documents
Culture Documents
v. 1.0
September, 2016
Users guide
Contact:
thegibbsproject@gmail.com
Abstract
Note
1. Introduction ................................................................................................ 6
2. Installation .................................................................................................. 6
3. Getting started ........................................................................................... 7
3.1 Using the Interface ...................................................................................................... 7
3.1.1 Connecting to the Databank file ............................................................................................ 9
3.1.2 Adding a compound ................................................................................................................ 9
3.1.2.1 Adding an image file of a compound .................................................................................................... 10
3.1.3 Deleting a compound ............................................................................................................ 11
3.1.4 Editing a compound .............................................................................................................. 11
3.1.5 Fragmentizing a compound into functional groups ................................................................ 12
3.1.6 Creating an estimation list ..................................................................................................... 15
3.2 Applying a function ................................................................................................... 17
4. Models and Properties ............................................................................ 18
4.1 Density (liquids) ......................................................................................................... 19
4.1.1 Group contribution................................................................................................................. 19
4.1.2 Correlation/Corresponding States Principle .......................................................................... 19
4.2 Viscosity (liquids) ...................................................................................................... 20
4.2.1 Group contribution................................................................................................................. 20
4.2.2 Correlation/Corresponding States Principles ........................................................................ 21
4.3 Viscosity (gases) ....................................................................................................... 21
4.3.1 Group contribution................................................................................................................. 21
4.3.2 Correlation/Corresponding States Principle .......................................................................... 21
4.4 Thermal conductivity (liquids) ................................................................................. 22
4.4.1 Group contribution................................................................................................................. 22
4.4.2 Correlation/Corresponding States Principle .......................................................................... 22
4.5 Thermal conductivity (gases) ................................................................................... 22
4.5.1 Group contribution................................................................................................................. 22
4.5.2 Correlation/Corresponding States Principles ........................................................................ 23
4.6 Heat capacity (ideal gases) ...................................................................................... 23
4.7 Heat capacity (liquids) .............................................................................................. 24
4.7.1 Group contribution................................................................................................................. 24
4.7.2 Correlation/Corresponding States Principles ........................................................................ 24
4.8 Normal melting temperature .................................................................................... 24
4.9 Normal boiling temperature ..................................................................................... 25
4.10 Critical temperature................................................................................................... 25
4.10.1 Group contribution ............................................................................................................ 25
4.10.2 Correlations ...................................................................................................................... 26
4.11 Critical pressure ........................................................................................................ 26
4.11.1 Group contribution ............................................................................................................ 26
4.11.2 Correlations ...................................................................................................................... 27
4.12 Critical volume ........................................................................................................... 27
4.12.1 Group contribution ............................................................................................................ 27
4.12.2 Correlations ...................................................................................................................... 28
4.13 Acentric factor ........................................................................................................... 28
4.13.1 Group contribution ............................................................................................................ 28
4.13.2 Correlation/Corresponding States Principle ...................................................................... 28
4.14 Surface tension .......................................................................................................... 29
4.14.1 Group contribution ............................................................................................................ 29
4.14.2 Correlation/Corresponding States Principles .................................................................... 29
4.15 Standard enthalpy of formation (at 298 K) .............................................................. 30
4.16 Standard Gibbs energy of formation (at 298 K) ..................................................... 30
4.17 Enthalpy of fusion ..................................................................................................... 30
4.18 Enthalpy of vaporization ........................................................................................... 31
4.18.1 Group contribution ............................................................................................................ 31
4.18.2 Correlation/Corresponding States Principle ...................................................................... 31
4.19 Entropy of vaporization (at Tb) ................................................................................ 32
4.19.1 Group contribution ............................................................................................................ 32
4.19.2 Correlation/Corresponding States Principle ...................................................................... 33
4.20 Vapor pressure .......................................................................................................... 33
4.20.1 Group contribution ............................................................................................................ 33
4.20.2 Correlation/Corresponding States Principle ...................................................................... 34
4.21 Van der Waals volume .............................................................................................. 34
5. Acknowledgements ................................................................................. 35
6. References ............................................................................................... 35
6
1. Introduction
OCTOPUS is a library of Excel functions developed to provide estimations
of physical and chemical properties of pure organic molecular compounds.
Values of these properties are often required for the solving of problems often
encountered by chemistry/chemical engineering students, researchers and
professionals.
A total of 215 functions (related to 154 estimation methods) was
implemented in Visual Basic for Applications (VBA) and can be directly accessed
in the spreadsheet environment. The properties covered in this version of the tool
include density (liquids), viscosity (liquids/gases), thermal conductivity
(liquids/gases), heat capacity (liquids/ideal gases), normal melting temperature,
normal boiling temperature, critical properties, acentric factor, surface tension
(liquids), standard enthalpy of formation, standard Gibbs energy of formation,
enthalpy of fusion, enthalpy of vaporization, entropy of vaporization, vapor
pressure and van der Waals volume. In general, the implemented methods are
based either on the Corresponding States Principle (CSP) and/or the group
contribution concept (GC) or are correlations that may be of general or of organic-
class specific application.
Our focus was to exclusively implement the models. Hence, this manual
does not contain detailed comments about them (e.g., organic-class applicability,
expected uncertainties, etc.). This information can be found in the original papers
or in reviews of thermodynamic models. Therefore, an appropriate use of this tool
requires a previous knowledge of the methods.
OCTOPUS has open source code and is distributed under the GNU Public
License v. 31.
2. Installation
This tool can be installed in any computer containing the Microsoft Office
software package (2010 or a more recent version). The distribution package
contains the following content:
1 http://www.gnu.org/licenses/.
2 It stores an image file named NOT_AVAILABLE which must not be moved or deleted.
3 These files must not be moved or deleted.
7
3. Getting started
Before learning about the estimation procedure, we strongly suggest that
you become familiar with the developed interface and its main features.
The following window will be displayed when you press the OCTOPUS
button (Figure 1):
8
Warning! An error will occur either if the folder Files is not in the same directory of the active
workbook or if this manual file has been moved from its original directory. Please check the
installation steps.
This window allows you to create a data bank which can store up to 32767
compounds whose properties you wish to estimate. In the next sections, you will
learn how to use its main functionalities, starting off with setting the connection
between the OCTOPUS interface and the Access Databank file.
The Databank file is distributed within the Files folder (check Section 2).
In the present section, you will learn how to connect the OCTOPUS interface to
the referred file. This connection allows you to transfer information between them.
Whenever you open the Excel workbook file and try to load the interface
shown in Figure 3 for the first time, you will notice that the Registered
compounds list is empty. If you click on the Import button, this list will be
automatically updated with the information stored in the Databank file.
Obviously, if this is the very first time you use this tool, the Databank file will be
empty and you wont need to import its data. In fact, as it will be shown further,
you will constantly need to update this file with the information you register in the
developed interface. This can be done by pressing the Export button.
In the following sections, you will learn how to create and edit your own
database. We suggest that you read the instructions carefully and try to
reproduce the examples shown.
The above fields correspond to some of the new compounds most relevant
information. In fact, the blue highlighted fields are required as input parameters
for the application of several functions from the OCTOPUS library. Therefore,
although a complete specification is not mandatory, we suggest that you include
as many information as possible when registering a compound. Occasionally, the
values of one or more properties may not be available for a substance. In these
cases, keep the referred field empty as shown above.
The acronyms of each property will be clearly understood when you click on
the .? button. The fields highlighted in green are locked, that is, you cannot
modify them. The ID field will be automatically specified when you click on the
New Compound button. The Yes and No check buttons will be determined
by the content of the Structures folder (check Section 2).
We highly recommend that you create an image file for each compound you
register in the database. This will be very helpful in the group fragmentation
procedures (Section 3.1.5). The image files must be inserted into the Structures
folder and have the .JPEG extension. Additionally, each of them must be named
with the compounds identification number, denoted by the ID field (Figure 4).
11
After this, the values of the highlighted buttons were automatically updated,
as presented in Figure 6:
Warning! After you complete the registration procedure, click on the Export button to
update the Databank file with the information you have just inserted. If you close the Excel
workbook file without pressing this button, your data bank will be lost.
You can select a compound in the Registered compounds list and click on
the Edit/Check Info. button to modify its information. The following window will
be displayed:
12
Before you can edit the selected compound (note that the fields in the
previous figure are grayed out), you must click on Edit information. The Clear
information button will erase all the registered information of the selected
compound. Once you have finished, do not forget to save the changes by clicking
on Save Information. To edit other compounds, you can use the highlighted
scrollbar to navigate through your data bank. Once you have completely finished
editing your database, return to the previous window and press on the Export
button to update the Access Databank file.
* If you are not interested in applying a group contribution method, you can skip to the next section.
13
You can filter the models that will be shown in the Organic molecular
compounds list by checking the properties you are interested in. The meaning of
the properties acronyms can be seen in the Nomenclature list. To start entering
the functional groups specifications, you must choose a method in the list and
press the Selected method button. For the Constantinou-Gani method1,2, the
following window will be displayed.
14
Notice that there are no second-order groups in this case. Finally, you must
save the fragmentation by clicking on the Save groups button. After that, select
another method and re-fragmentize the structure of the selected compound using
the other methods functional groups. Then, choose another compound and
repeat this whole process. To conclude, return to the Database interface (Figure
4) and click on the Export button to transfer the fragmentations to the Access
file.
Once you have created your database and have specified all the relevant
compounds information, you can return to the window presented in Figure 4 and
create an estimation list. Doing this will be very helpful in applying the
implemented functions.
To create an estimation list, you must select compounds in the Registered
compounds list and press the Add to list button. The Estimation list box will
be filled with the selected compounds, as presented in Figure 11.
16
Warning! Although when registering a compound you have entered its properties values
according to the units shown in Figure 4 (e.g., pressure in [bar], molar volumes in [cm3/mol],
etc.), the implemented functions require the input variables to be in the IS units. Thus, it is
really important that you create an estimation list, since the values of the properties printed by
the OCTOPUS interface are the appropriate ones for a function application.
17
The estimation procedure is very simple. First, you must choose a property
and obtain its acronym from Table 1 (Section 4.1). Then, you must select the
appropriate model (that will be used to estimate this property) and obtain its
acronym. The acronyms of all the group contribution methods are shown in the
Identification column from the list of methods presented in Figure 8. For the
methods based in the Corresponding States Principle or in correlations, you can
check the next section or become familiar to the rule we adopted to generate the
acronyms1. Then, the appropriate formula must be applied in a spreadsheet cell.
The syntax for a formula application depends on the acronyms for the property
and the method. The general formula is:
For the Tc_CG function, the only input parameter is the identification
number of the compound (variable ID_Comp). If we apply this function to
estimate the critical temperature of Propan-2-one (ID_Comp = 1; check Figure
12), we obtain the following result:
1 If the model was proposed by only one author, the acronym is equal to the name of that author (e.g.,
Riedel, Vetere, Somayajulu); if the model had 2 or 3 authors, the acronym equals the initial letter of
each author name (e.g., AW denotes the method proposed Ambrose and Walton (1989); MRR denotes
the method proposed by Moller, Rarey and Ramjugernath (2008)); if the method was proposed by more four
or more authors, the acronym equals the name of the first author from the published paper (e.g., Ponce
denotes the method proposed by Ponce et al. (2013)).
18
Critical temperature Tc 1 18
Critical pressure Pc 1 13
Critical volume Vc 3 13
Total 84 131
The column Acronym denotes the acronyms adopted for each property
covered by this tool (check the previous section). Probably, you will consult this
table very often until you become familiar with the adopted nomenclature.
Although we have focused on implementing most of the very widely used
methods, we have included several recently published models in the OCTOPUS
library.
The following sections contain more information about the implemented
library. You can skip to the method you are interested in applying.
19
Nomenclature: ID_Comp = Compound's identification number (in the database); T = Temperature; MM = Molar mass; Tb =
Normal boiling temperature.
a
These not necessarily correspond to the original authors' papers. Occasionally, these have not been found.
b
It considers the group parameters of the GCVOL60 method in combination to the refit proposed by Pratas et al (2011).
c
It considers the group parameters of the GCVOLOL60 method in combination to the refit proposed by Pratas et al (2011).
d
Estimates this property at T = 298 K.
e
Estimates this property at T = Tb.
Method
Function syntax Inputs Referencesa
Authors Acronym
Mchaweh et al. simplifiedMchaweh DensL_simplifiedMchawehc T, MM, Tc, Vc, Omega 20,21
Nomenclature: ID_CompClass = Compound's class identification number; T = Temperature; MM = Molar mass; Tb = Normal boiling temperature;
Tc = Critical temperature; Pc = Critical pressure; Vc = Critical volume; Zc = Critical compressibility factor; Zra = Adjustable parameter proposer by
the authors; Omega = Acentric factor; Mi = Modulus of the dipole moment vector; Tref = Reference temperature; DensLTref = Liquid density at
Tref.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
b
1) Nonpolar; 2) Polar; 3) Polar containing a hydroxyl group.
c
This corresponds to the SNM0 model tested by Mulero, Cachadia and Parra (2006).
d
Estimates this property at T = Tb.
Nomenclature: ID_CompClass = Compound's class identification number; ID_EsterClass = Ester class identification number; ID_Comp
= Compound's identification number (in the database); T = Temperature; MM = Molar mass; Tb = Normal boiling temperature; Tc = Critical
temperature; Pc = Critical pressure; DensL293: Liquid density at T = 293 K; DensL = Liquid density at the temperature of interest.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
b
1) Hydrocarbon; 2) Halogenated hydrocarbon; 3) Benzene derivative; 4) Halogenated benzene derivative; 5) Alcohol; 6) Organic acid; 7)
Ether/Ketone/Aldehyde/Acetate; 8) Phenol; 9) Miscellaneous.
c
1) Phenol; 2) Acid; 3) Others.
d
1) Fatty acid; 2) Alcohol; 3) Ester; 4) Acylglycerol.
e
0) Not an ester; 1) Methyl esters; 2) Ethyl esters; 3) Propyl esters; 4) Butyl esters.
f
Estimates this property at T = 293 K.
21
Nomenclature: T = Temperature; MM = Molar mass; Tm = Normal melting temperature; Tc = Critical temperature; Pc = Critical
pressure; Vc = Critical volume; Omega = Acentric factor; Tref = Reference temperature; DensLTref = Liquid density at Tref.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
Nomenclature: ID_Comp = Compound's identification number (in the database); T = Temperature; MM = Molar
mass; Tc = Critical temperature; Pc = Critical pressure; Mi = Modulus of the dipole moment vector.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
Lakshmir/Prasad LP LambdaL_LP T, MM 37
Nomenclature: ID_Comp = Compound's identification number (in the database); T = Temperature; MM = Molar mass; Tb = Normal boiling
temperature; Tc = Critical temperature; DensLTb = Liquid density at T = Tb; DeltaSvTb = Entropy of vaporization at T = Tb; ViscG = Gas
viscosity at the temperature of interest; CpIG = Ideal gas heat capacity at the temperature of interest.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
Misic/Thodos MT LambdaG_MT b
ID_CompClass , T, MM, Tc, Pc, CpIG 15,41
Nomenclature: ID_CompClass = Compound's class identification number; T = Temperature; MM = Molar mass; Tc = Critical
temperature; Pc = Critical pressure; Vc = Critical volume; Zc = Critical compressibility factor; Omega = Acentric factor; ViscG =
Gas viscosity at the temperature of interest; CpIG = Ideal gas heat capacity at the temperature of interest.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
b
1) Methane/Naphthalene/Aromatic hydrocarbon; 2) Other hydrocarbon.
KolskaH CpL_KolskaH b
ID_Comp, T 48
Kolska et al.
KolskaNH CpL_KolskaNHc ID_Comp, T 48
Chueh/Swanson CS CpL293_CS e
ID_Comp 54
Nomenclature: T = Temperature; Tc = Critical temperature; Omega = Acentric factor; CpIG = Ideal gas heat capacity at
the temperature of interest.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
Nomenclature: ID_Comp = Compound's identification number (in the database); MM = Molar mass; Vvdw
= van der Waals volume.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
Method Function
Inputs Referencesa
Authors Acronym syntax
Lydersen Lydersen Tc_Lydersen ID_Comp, Tb 15
Tu Tu Tc_Tu ID_Comp 67
Nomenclature: ID_Comp = Compound's identification number (in the database); MM = Molar mass; Tb = Normal boiling
temperature; Nr = Number of rings in the molecule; DeltaPlatt = Topological parameter proposed by the author.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
4.10.2 Correlations
Method Function
Inputs Referencesa
Authors Acronym syntax
Wilson/Jasperson WJ Pc_WJ ID_Comp, Tc, Nr 6
Nomenclature: ID_Comp = Compound's identification number (in the database); MM = Molar mass; Tb = Normal boiling
temperature; Tc = Critical temperature; Nat = Number of atoms in the molecule; Nr = Number of rings in the molecule;
DeltaPlatt = Topological parameter proposed by the author.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
4.11.2 Correlations
Method Function
Inputs Referencesa
Authors Acronym syntax
Somayajulu Somayajulu Vc_Somayajulu ID_Comp 74
Nomenclature: ID_Comp = Compound's identification number (in the database); MM = Molar mass.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
4.12.2 Correlations
Nomenclature: ID_Comp = Compound's identification number (in the database); DeltaPlatt = Topological
parameter suggested by the authors.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
b
Knotts1 SigmaL_Knotts1 ID_Comp, MM, DensL, DensV
Knotts et al. 85
c
Knotts2 SigmaL_Knotts2 ID_Comp, MM, DensL, DensV
Nomenclature: ID_Comp = Compound's identification number (in the database); MM = Molar mass; DensL = Liquid
density at the temperature of interest; DensV = Vapor density at the temperature of interest.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
b
It considers the parameters obtained by the use of the training set with an uncertainty <5%
c
It considers the parameters obtained by the use of the training set with an uncertainty <1%
Table 28 - Available GC methods for estimating standard Gibbs energies of formation at 298 K
Method
Function syntax Inputs Referencesa
Authors Acronym
Joback/Reid JR DeltaGf298_JR ID_Comp 6,22
Method
Function syntax Inputs Referencesa
Authors Acronym
Vetere2 DeltaHvTb_Vetere2b ID_CompClassd, MM, Tb
b
Vetere3 DeltaHvTb_Vetere3 ID_CompClasse, Tb, Tc, Pc
Liu Liu DeltaHvTb_Liub Tb, Tc, Pc 105
Nomenclature: ID_CompClass = Compound's class identification number; ID_PairRF = Pair of reference fluids
identification number; T = Temperature; MM = Molar mass; Tb = Normal boiling temperature; Tc = Critical temperature; Pc
= Critical pressure; Omega = Acentric factor.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
b
Estimates this property at T = Tb.
c
1) Ethylcyclopentane/Carbon monoxide; 2) R1/R2 (hypothetical fluids).
d
1) Hydrocarbon/CCl4; 2) Alcohol; 3) Ester; 4) Other (polar).
e
1) C2+/Alcohol/Dimerizing compound; 2) Hydrocarbon/Other (polar); 3) H2/He.
Nomenclature: ID_CompClass = Compound's class identification number; MM = Molar mass; Tb = Normal boiling
temperature; Tc = Critical temperature; Pc = Critical pressure.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
b
1) Hydrocarbon/CCl4; 2) Alcohol; 3) Ester; 4) Other (polar).
c
1) C2+/Alcohol/Dimerizing compound; 2) Hydrocarbon/Other (polar); 3) H2/He.
Method Function
Inputs Referencesa
Authors Acronym syntax
Koslka/Ruzicka/Gani KRG DeltaSvTb_KRG ID_Comp
Hoshino/Nagahama/Hirata HNH DeltaSvTb_HNH ID_Comp
Ma/Zhao MZ DeltaSvTb_MZ ID_Comp
Nomenclature: ID_Comp = Compound's identification number (in the database).
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
c
Vetere3 DeltaSvTb_Vetere3 ID_CompClass , Tb, Tc, Pc
Liu Liu DeltaSvTb_Liu Tb, Tc, Pc 105
Nomenclature: ID_CompClass = Compound's class identification number; MM = Molar mass; Tb = Normal boiling
temperature; Tc = Critical temperature; Pc = Critical pressure.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
b
1) Hydrocarbon/CCl4; 2) Alcohol; 3) Ester; 4) Other (polar).
c
1) C2+/Alcohol/Dimerizing compound; 2) Hydrocarbon/Other (polar); 3) H2/He.
Method Function
Inputs Referencesa
Authors Acronym syntax
Nannoolal et al. Nannoolal Pvap_Nannoolal ID_Comp, T, Tb 112
Nomenclature: ID_CompClass = Compound's class identification number; ID_EsterClass = Ester class identification number; ID_Comp =
Compound's identification number (in the database); T = Temperature; MM = Molar mass; Tb = Normal boiling temperature; Tc = Critical
temperature.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
b
1) Acid; 2) Alcohol; 3) Phenol; 4) Other
c
1) Fatty ester; 2) Acylglycerol; 3) Fatty acid; 4) Alcohol; 5) Hydrocarbon
d
0) Not an ester; 1) Methyl ester; 2) Ethyl ester; 3) Propyl ester; 4) Butyl ester
Ambrose/Patel AP Pvap_AP c
ID_PairRF , T, Tc, Pc, Omega 117
Nomenclature: ID_CompClass = Compound's class identification number; ID_PairRF = Pair of reference fluids identification
number; T = Temperature; MM = Molar mass; Tb = Normal boiling temperature; Tc = Critical temperature; Pc = Critical pressure;
Omega = Acentric factor.
a
These not necessarily correspond to the original authors' papers. In some cases, these have not been found.
b
1) Nonpolar; 2) Acid; 3) Alcohol; 4) Glycol; 5) Water/Ammonia/Polar nonassociated
c
1) Propane/Octane; 2) Benzene/Pentafluorotoluene
d
1) Nonpolar; 2) Polar; 3) Water/Alcohol; 4) H2; 5) He; 6) Ne
5. Acknowledgements
We thank Professor Angel Mulero from the University of Extremadura
(Extremadura, Spain) and Professor Richard R. Rowley from the Brigham Young
University (Utah, USA) for kindly replying our e-mails during the development of
this tool.
6. References
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Properties of Pure Compounds. AIChE J. 1994, 40 (10), 1697.
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the Liquid Molar Volume at 298 K Using a New Group Contribution Method. Fluid
Phase Equilib. 1995, 103, 11.
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Prediction of Liquid Densities as a Function of Temperature for Solvents,
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Method GCVOL for the Prediction of Pure Compound Liquid Densities. Ind. Eng.
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(5) Pratas, M. J.; Freitas, S. V.D.; Oliveira, M. B.; Monteiro, S. C.; Lima, . S.;
Coutinho, J. A. P. Biodiesel Density: Experimental Measurements and Prediction
Models. Energy and Fuels 2011, 25, 2333.
(6) Poling, B. E.; Prausnitz, J. M.; OConnel, J. P. The Properties of Gases And
Liquids, 5th ed.; McGraw-Hill, 2001.
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15 (4), 514.
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1127.
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Chem. Eng. Data 1973, 18 (2), 230.
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Fluids at Reservoir Conditions. Ind. Eng. Chem. Res. 1995, 34 (11), 3981.
36
11 (4), 509.
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(102) Cachadia, I.; Mulero, A. New Corresponding States Model for the Estimation of
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