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Hugo Hernandez
ForsChem Research, 050030 Medellin, Colombia
hugo.hernandez@forschem.org
doi: 10.13140/RG.2.2.36384.07681
Abstract
Clausius definition of the molecular sphere of action has proved to be a valuable concept for
describing and understanding the behavior of matter from a molecular point of view. In the
present report, the effect of crowding on the mean sphere of action between Lennard-Jones
molecules is investigated by molecular dynamics simulation. A crowding function is defined in
order to quantify the effect of molecular crowding on the spheres of action. For single
component systems at high temperatures, it was possible to identify three different cases of
crowding: 1) an ideal gas case, where molecules do not affect the sphere of action of their
neighbors, 2) a non-ideal gas case, where the molecular interaction potential of neighbor
molecules interferes causing a distortion in the sphere of action, and 3) a dense case, where
the sphere of action of neighbor molecules overlap, resulting in a permanent collision condition
between neighbors. The results obtained can be generalized for multicomponent systems
using an extension of Lorentz and Berthelot rules of mixing for calculating the overall Lennard-
Jones parameters of the mixture. Using this approach, it is possible to determine the
conditions for transition from the ideal gas to the non-ideal gas behavior, and also from the
non-ideal gas to the dense behavior. An example is presented for air, where an extended
phase-diagram is obtained, showing that the dense behavior approximately corresponds to the
supercritical phase. It was found that the transition density to the dense phase corresponds to
the density of the critical point of air. It is also observed that at ambient conditions, air always
behave as an ideal gas.
Keywords
Clausius, Crowding function, Dense behavior, Ideal gas, Lennard-Jones, Molecular crowding,
Non-ideal gas, Phase diagram, Sphere of action, Supercritical fluids.
1. Introduction
Previously,[1] it was shown that the concept of the radius of the sphere of action between
molecules, proposed by Clausius in the 1850s,[2] can be used for the estimation of molecular
collision distances and collision kinetics. Although difficult to measure experimentally, the
radius of the sphere of action of low-density systems can be obtained from molecular
simulations for any given interaction potential model and its corresponding interaction
parameters. It was also previously proposed[1] that as the density of the systems increase, a
certain correction function is needed because the presence of other molecules modifies the
net molecular interaction.
The purpose of the present work is to investigate the nature of such correction function, and
to extend the use of Clausius concept of the sphere of action in crowded gaseous systems.
It is also important to remark some of Clausius ideas about the density of molecular
systems:[2]
(1.1)
where is the mean distance between neighbouring molecules and is the number density of
the system. The number density is represented in bold font, because following Clausius
original nomenclature, is the radius of the sphere of action.
Let us consider the system depicted in Figure 1, which is a modification of the system previously
considered for low-density systems.[1] The system is composed by 3 molecules. The first
molecule is the reference molecule, and both position and velocities of other molecules will be
expressed relative to this particular molecule. There is a second molecule, identical to molecule
1, whose center is placed at a distance with respect to the center of molecule 1, which
corresponds to the mean distance between neighbouring molecules (Eq. 1.1). Normally, this
second molecule will be moving at random velocities and located at a random position around
molecule 1; however, it will be assumed that molecule 2 remains stationary at a distance ,
aligned horizontally with respect to molecule 1. Even though this is not realistic, on average
that will be the most probable position for a molecule around molecule 1. A third molecule is
considered to move vertically in direction of the two molecules. The expected closest distance
between the centers of molecules 1 and 3 will be given by , whereas the expected closest
distance between molecules 2 and 3 will be given by . Both expected closest distances are
related by:
(2.1)
where . If were larger than , the naming of the molecules would simply be
inverted to meet the condition (2.1).
Figure 1. Graphical representation of the possible effect of two molecules on a third molecule.
The distance between molecules 1 and 2 is given by . The expected closest distances between
molecule 3 and molecules 1 and 2 are given by and , respectively, where . The
deviations in the expected path of molecule 3 refer to the net interaction with molecule 1.
Given that molecules 1 and 2 are identical, it is expected that their interaction forces on
molecule 3 partially counteract, yielding a weaker net interaction and thus, a smaller radius of
the sphere of action. The equation proposed for describing such behavior, in general terms
is:[1]
( ) ( )( )
(2.2)
Please notice that refers to the maximum molecular density of the system in the gaseous
state. Beyond this density, the permanent collision between closest neighbors is unavoidable,
causing the motion of the molecules in the system to be highly constrained and potentially
leading to phase change. This dense state, however, remains fluid.
A molecular dynamics (MD) simulation for the system represented in Figure 1 is performed
considering a Lennard-Jones interaction potential with parameters (equilibrium distance)
and (depth of potential well). The simulation was performed in R (https://cran.r-project.org/),
and the algorithm used is presented in Appendix 1. The results obtained for different reduced
relative kinetic energies are summarized in Figure 2.
Solving for the crowding function ( ) from Eq. (2.2) results in:
( )
( )
(2.3)
Figure 3 presents the transformation into the crowding function using Eq. (2.3) of some of the
results shown in Figure 2. The star superscript (*) indicates a reduced dimensionless variable.
Figure 3. Behavior of the crowding function ( ) for different reduced number densities
( ) and reduced relative kinetic energies ( ) from MD simulation data
i) An ideal gas region, where the value of the crowding function is zero, ( )
ii) A non-ideal gas region, where the value of the crowding function is ( )
iii) A dense region, where the value of the crowding function is one, ( )
The non-ideal gas region can be described using the following empirical function:
( ) ( ) ( ( ) ( ))
(2.4)
where , and are empirical parameters, which are function of the reduced relative kinetic
energy of the molecules, . Those parameters were fitted by least-squares minimization using
non-linear empirical functions and MD simulation data, yielding the following expressions:
( )
( )
(2.5)
( )
( )
(2.6)
( ) ( ( ( )) )
(2.7)
( ) [ ( )]
(2.8)
and therefore:
( )
( ( ( )) )
(2.9)
On the other hand, the transition from the non-ideal gas to the dense phase is expected to
occur at , which for Lennard-Jones interactions, it will be:
( )
( )
(2.10)
Eq. (2.9) is graphically depicted in Figure 4, as a function of the reduced relative kinetic energy
of the molecules. This result is compared with the corresponding values observed directly from
MD simulation.
Figure 4. Reduced density transitions for different reduced relative kinetic energies in systems
with Lennard-Jones interaction: i) From ideal to non-ideal gas (blue solid line: calculated from
Eq. (2.9), red dots: extracted from MD simulation) ii) From non-ideal gas to dense behavior
(green dashed line)
Even though the fit obtained in the calculation of the transition between ideal and non-ideal
gas behavior is only about 53%, the general behavior is correctly described. Such low fit is
caused by the resolution used in the values of the reduced expected closest distance, which for
larger relative kinetic energies resulted in larger numerical errors.
The behavior of the transition density from ideal to non-ideal behavior can be explained by the
behavior of Clausius sphere of action and of the interaction potential. When the relative kinetic
energy is close to zero, the spheres of action are larger and therefore the transition takes place
at lower densities. As the kinetic energy increases, Clausius spheres of action become smaller
allowing higher values of the transition density. At a certain point, when the kinetic energy is
even higher, the spheres of action approach their minimum size and the motion of the
molecules becomes less dependent of the interaction potential, reaching an almost constant
reduced transition density. This effect is also observed in Figure 5, which shows the transition
point ratios in a plot of the mean distance between molecules to the corresponding radius of
the sphere of action versus the reduced relative kinetic energy. Such ratio can be obtained
from MD simulation or can be calculated using the following expression:
( ( ( )) )
[ ( )] ( )
(2.11)
Figure 5. Transition ratios of mean distance between molecules to radius of the sphere of
action ( ) for different reduced relative kinetic energies in systems with Lennard-Jones
interaction. i) From ideal to non-ideal gas (blue solid line: calculated from Eq. (2.11), red dots:
extracted from MD simulation) ii) From non-ideal gas to dense behavior (green dashed line)
The shape described by the transition from ideal to non-ideal gas behavior clearly resembles
the shape of the interaction potential. In this sense, the minimum value of the ratio
corresponds to the point where the net interaction momentum is minimum; that is, when the
interference of neighbor molecules on the molecular interaction is maximum.
It can also be observed in Figure 5 that the transition from ideal to non-ideal gas behavior takes
place when the mean distance between molecules is in the range from 2.5 to 3.5 times the
radius of the sphere of action. In other words, when the distance between molecules is larger
than 3.5 times the radius of the sphere of action, no interference effect is expected from
neighbor molecules.
Now, given that the reduced relative kinetic energy can be expressed in terms of the system
temperature and the standard Maxwell-Boltzmann random variable ,[3] as:
(2.12)
then, from Eq. (2.9):
( )
( ) ( )
( ( ) )
( )
( ( )) ( )
(2.13)
The last expression is obtained by solving the corresponding integral of the Maxwell-
Boltzmann distribution for the non-linear function inside the expected value operator.
The behavior of the reduced transition densities as a function of the temperature of the
system, given by Eq. (2.10) and (2.13) is presented in Figure 6.
For practical purposes (high temperatures), it can be seen that the non-ideal gas behavior in
pure systems with Lennard-Jones interaction is observed for mass densities in the range from
about to , where is the mass of a single molecule. Table 1 presents the
transition mass densities for different compounds with Lennard-Jones interaction.
Figure 6. Reduced density transitions for different reduced thermal energies in systems with
Lennard-Jones interaction: i) From ideal to non-ideal gas (blue solid line: calculated from Eq.
2.13) ii) From non-ideal gas to dense behavior (green dashed line: calculated from Eq. 2.10)
The results presented in Section 2 were obtained considering that all molecules involved are
identical. In multicomponent systems this is no longer the case, and it is therefore necessary to
consider that all 3 molecules represented in Figure 1 might be different species. In general, it is
possible to say that the number of different possible permutations of molecules in a system
with different components is:
(3.1)
For each of these possibilities, a different radius of the sphere of action will be obtained as a
result of the different interaction between molecules. Also, each possibility will take place with
a different probability which will depend on the composition of the system.
Even though it is possible to perform the simulation for all possible permutations, and calculate
the mean radius of the sphere of action for a system with any given number of components
and any given composition, it is cumbersome to find a generalized mathematical expression
valid for any arbitrary system.
(3.2)
(3.3)
where and are the overall Lennard-Jones parameters for the multicomponent system
with different components, and is the molar fraction of each component .
Using these overall parameters with the equations obtained in Section 2, it is now possible to
estimate the mean radius of the spheres of action for the multicomponent system. Let us
consider for example the transition density from ideal to non-ideal gas behavior in air with the
composition given in Table 2.
The overall Lennard-Jones parameters of the system using the proposed mixing rules (Eq. 3.2
and 3.3) will be:
(3.4)
(3.5)
The transition density from ideal to non-ideal behavior will be (from Eq. 2.13):
( )
( ) ( )
( ( )) ( )
(3.6)
( )
(3.7)
(3.8)
Then, the mass density transition from ideal to non-ideal gas behavior for air at room
temperature is .
Since the mass density of air at sea level (maximum density on Earth) is about , it is safe
to say that at ambient conditions, air behaves as an ideal gas.
Now, the minimum pressure at which non-ideal behavior should begin to be observed for air at
room temperature (298.15 K) will be:
( ) ( )
( ( )) ( )
(3.9)
On the other hand, it is also possible to estimate the transition density from non-ideal gas to
dense behavior (from Eq. 2.10):
( ) ( )
(3.10)
Thus,
( )
(3.11)
and the corresponding transition mass density of air between the non-ideal gas behavior and
the dense behavior is .
Considering that the non-ideal gas behavior of the system can be approximately described by
the following van der Waals equation of state in terms of the Lennard-Jones parameters:[4]
( )( )
(3.12)
then, the system pressure at which the transition from non-ideal gas behavior to the dense
behavior can be described by the following expression:
( )
(3.13)
[ ] [ ]
(3.14)
From Eq. (3.9) and (3.14), and using data from a conventional air phase diagram,[7] the
following extended phase diagram can be obtained (Figure 7):
Figure 7. Extended phase diagram for air, including the ideal gas, non-ideal gas and dense
regions. Red line: Transition between non-ideal gas and dense regions. Green line: Transition
between ideal and non-ideal gas. Blue line: Transition between gas and liquid phases. Purple
line: Transition between liquid and solid phases. Black dashed line: Transition from supercritical
to liquid phase. Black dot: Critical point. Green dot: Normal conditions (293.15 K, 0.101 MPa).
The model developed so far for multicomponent systems shows that the predicted transition
density from non-ideal gas to dense behavior corresponds to the density at the critical point. It
can also be observed that the dense behavior is almost equivalent to the supercritical fluid
condition.
If mean distances between neighbor molecules smaller than those considered in the present
report are used in the simulations, it is possible that new relationships arise from the behavior
of Clausius spheres of action which might describe the transition from gas to liquid, from liquid
to solid, and from the dense (supercritical) region to the liquid or solid phases. This, however, is
the focus of future research.
4. Conclusion
In the present report, it was possible to show that the density and temperature of a system
have a significant effect on the radii of Clausius molecular spheres of action. The effect of
density can be described by a crowding function, representing the effect of interference in
interaction potentials between neighbor molecules. Molecular dynamic simulations were
performed for understanding the behavior of the crowding functions. As a result, three
different regions were identified in gaseous systems: Ideal-gas, non-ideal gas and dense
(supercritical). The analysis of simulation results allowed predicting transition conditions
between these regions in pure systems (Eq. 2.10 and 2.13). For multicomponent systems, simple
mixing rules (Eq. 3.2 and 3.3) can be used for calculating equivalent overall Lennard-Jones
parameters. An example is presented for air, and the corresponding transition conditions
obtained are summarized in an extended P-T phase diagram (Figure 7).
Acknowledgments
The author gratefully acknowledges the helpful suggestions given by Prof. Jaime Aguirre
(Universidad Nacional de Colombia) and Prof. Silvia Ochoa (Universidad de Antioquia) for
improving the manuscript.
This research did not receive any specific grant from funding agencies in the public,
commercial, or not-for-profit sectors.
References
[1] Hernandez, H. (2017). Clausius sphere of action for different intermolecular potentials.
ForsChem Research Reports 2017-10. doi: 10.13140/RG.2.2.25246.23363
[2] Clausius, R. V. (1859). X. On the mean length of the paths described by the separate
molecules of gaseous bodies on the occurrence of molecular motion: together with some other
remarks upon the mechanical theory of heat. The London, Edinburgh, and Dublin Philosophical
Magazine and Journal of Science, 17(112), 81-91.
[5] Lorentz, H. A. (1881). Ueber die Anwendung des Satzes vom Virial in der kinetischen Theorie
der Gase. Annalen der Physik, 248(1), 127-136.
[7] Wolfram|Alpha Knowledgebase, Air Phase Diagram (2017). Accessed: 29/09/2017. Link:
http://www.wolframalpha.com/input/?i=%5B%2F%2Fsubstance:air%2F%2F%5D+phase+diagram.
#Main script
rK=c(0.02,0.04,0.1,0.14,0.2,0.4,0.6,0.8,1,2,3,4,5,6,7,8,9,10,15,20)
#Initialization of reduced kinetic energy vector
rEr=1.256*(1+0.4264*log(0.7794+1/rK)) #Mean radius of sphere of action
rrho=array(0, dim=c(20,20)) #Initialization of radius of sphere vector
rl=array(0, dim=c(20,20)) #Init. of reduced mean distance between molecules 1 and 2
niter=4000 #Set number of iterations in MD simulation
for (i in 1:20){ #Iteration loop for reduced kinetic energy
for (k in 1:20){ #Iteration loop for red. mean distance between molecules
rl[i,k]=2+(round(4*rEr[i]-2)*k/20) #Set reduced mean distance between molecules
for (j in 1:300) { #Iteration loop for initial closest reduced distance
rd=min(rl[i,k]/2,round(100*rEr[i])/100+0.01)-((j-1)/200)
#Set closest reduced distance (from largest to smallest)
coll=collision2(rd,rK[i],rl[i,k],niter) #Simulate single collision for these conditions
if (coll>0) { #If collision takes place
rrho[i,k]=rd #Set the reduced radius of sphere of action as the
#reduced closest distance
break #Stop the loop for closest reduced distances
}
}
}
plot(rl[i,],rrho[i,]) #Plot the results
}