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 Aqueous Phase
Adsorption
Theory, Simulations and Experiments
http://taylorandfrancis.com
 Aqueous Phase
Adsorption
Theory, Simulations and Experiments

Edited by
Jayant K. Singh
Nishith Verma
CRC Press
Taylor & Francis Group
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Boca Raton, FL 33487-2742

© 2019 by Taylor & Francis Group, LLC

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Library of Congress Cataloging‑in‑Publication Data

Names: Singh, Jayant K., editor. | Verma, Nishith, editor.

Title: Aqueous phase adsorption : theory, simulations, and experiments /
edited by Jayant K Singh, Nishith Verma.
Description: Boca Raton : Taylor & Francis, CRC Press, 2019. | Includes
bibliographical references and index.
Identifiers: LCCN 2018018459| ISBN 9781138575219 (hardback : alk. paper) |
ISBN 9781351272520 (ebook)
Subjects: LCSH: Adsorption.
Classification: LCC TP156.A35 A77 2019 | DDC 660/.284235--dc23
LC record available at https://lccn.loc.gov/2018018459

Visit the Taylor & Francis Web site at

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http://www.crcpress.com
Contents

Preface..................................................................................................................... vii
Editors.......................................................................................................................xi
Contributors.......................................................................................................... xiii

1. Theory, Molecular, Mesoscopic Simulations, and Experimental

Techniques of Aqueous Phase Adsorption................................................1
Jayant K. Singh and Nishith Verma

2. Graphene Nanopores-Based Separation of Impurities

from Aqueous Medium................................................................................43
Anitha Kommu and Jayant K. Singh

3. Computational Chemistry Assisted Simulation for Metal Ion

Separation in the Aqueous-Organic Biphasic Systems......................... 69
Sk. Musharaf Ali, Anil Boda, Ashish Kumar Singha Deb, and Pooja Sahu

4. Aqueous Separation in Metal-Organic Frameworks:

From Experiments to Simulations........................................................... 111
Krishna M. Gupta and Jianwen Jiang

5. Coating of Nanoparticles in Aqueous Solutions: Insights

from Molecular Dynamics Simulations................................................. 135
Zuzana Benková and M. Natália D. S. Cordeiro

6. Lattice-Boltzmann Modeling of Adsorption Breakthrough

in Packed Beds............................................................................................. 159
Nishith Verma

7. Improved Removal of Toxic Contaminants in Water by Green

Adsorbents: Nanozeolite and Metal-Nanozeolite for the
Removal of Heavy Metals and Phenolic Compounds......................... 181
Thi-Huong Pham and Byeong-Kyu Lee

8. Abiotic Removal with Adsorption and Photocatalytic Reaction....... 213

Robert Chang-Tang Chang, Bor-Yann Chen, Ke-Fu Zhou, Qiao-Jie Yu,
Xiao-Dan Xie, Mridula P. Menon, and Arun Kumar Subramani

v
vi Contents

9. Revalorization of Agro-Food Residues as Bioadsorbents

for Wastewater Treatment.......................................................................... 249
Gassan Hodaifa, Cristina Agabo García, and Santiago Rodriguez-Perez

10. Adsorption on Activated Carbon: Role of Surface Chemistry

in Water Purification................................................................................... 283
Vivekanand Gaur

Index...................................................................................................................... 301
Preface

Adsorption is a commonly used technique for treating wastewater. It is

energy efficient and considered to be effective for removing a wide range
of pollutants from water, including arsenic, fluoride, volatile organic com-
pounds, and toxic metals. With the increasing production of a number of
pharmaceutical, healthcare, and agricultural products, and simultaneously
continuous decrease in the global water table, several aqueous species have
been identified as “emerging pollutants,” for which new adsorbents are yet
to be produced.
Through various chapters contributed by accomplished researchers work-
ing in the broad area of adsorption, this book provides necessary funda-
mental backgrounds required for an academician, industrial scientist, or
engineer to initiate studies in this area. In particular, this book covers theo-
retical aspects of adsorption, including an introduction to molecular simula-
tions and other numerical techniques that have become extremely useful as
an engineering tool in recent times to understand the interplay of different
mechanistic steps of adsorption. Further, the book provides brief experimen-
tal methodologies to use, test, and evaluate different types of adsorbents for
water pollutants.
The editors of this book want to make it clear that this book is not to be con-
sidered as a textbook for undergraduate students who want to get ­firsthand
experience of adsorption experiments or/and simulations, nor it is there to
provide ready-made solutions to the buyers of wastewater treatment plants.
Rather, the book is useful to those who want to make an advancement in
developing novel remediation technologies, as its chapters systematically
span the mechanistic steps of adsorption in water under batch and flow
conditions and a wide range of applications in the critical areas of aqueous
phase adsorption via the illustration of various case studies.
Chapter 1 provides a solid background of the fundamentals of adsorption,
including thermodynamic aspects of adsorption and classical adsorption
isotherms used to explain the adsorption data. It moves on to describe the
efficacy of computer modeling currently used to understand complex adsorp-
tion systems at a fundamental (molecular) level. It also shows how computer
simulations can be used as a means to predict the adsorption behavior and
other relevant materials properties, from the microscopic detail viz. atomic
masses and atomic charges, etc., via the Monte Carlo and molecular dynam-
ics approaches. The second part of Chapter 1 provides an overview of the
mesoscopic lattice Boltzmann approach, including computational steps to
predict flow field and associated concentration and temperature profiles in a
packed bed adsorber. The chapter ends with a brief description of the experi-
mental methodologies in practice to measure the aqueous phase adsorption

vii
viii Preface

capacity of a solid under batch or static conditions, breakthrough experi-

ments, and challenges in conducting the adsorption tests.
Chapter 2 presents an overview of graphene and graphene oxide-based
materials for membrane separation process. In particular, this chapter sum-
marizes key molecular simulations studies illustrating the high selectively
and mass transport of graphene-based membranes. Chapter 3 illustrates
the use of computational chemistry and molecular dynamic simulations in
understanding the ligand-aided metal ion transfer process aiming towards
separation of metal ions from the aqueous phase using liquid-liquid sepa-
ration. The chapter explains how interaction strength of ligand molecules
with radionuclide can be calculated from computational chemistry calcula-
tions that can aid in selecting suitable extractants. Chapter 4 presents recent
experimental and simulation studies using metal organic frameworks.
In particular, molecular simulation studies are presented demonstrating
the use of MOFs in the removal of organic and inorganic molecules from
aqueous phase. Chapter 5 presents the use of liquid adsorption to modu-
late the properties of coating on nanoparticles for various applications. The
chapter provides an insight into the coating of polymer chains on inorganic
nanoparticles and its effect on the aggregation and dispersion properties of
nanoparticles. In addition, solvation behavior of coated nanoparticles are
also discussed.
Chapter 6 describes the computational steps of implementing the lattice
Boltzmann methods–based models for predicting the adsorption break-
through profiles in a tubular column packed with porous adsorbent particles.
The description is sufficient in that readers can easily grasp the development
of mesoscopic or lattice Boltzmann methods–based model equations analo-
gous to the macroscopic conservation equations for the tubular packed bed
adsorber. The chapter goes on to provide detailed numerical scheme, model
validation, and the characteristic simulation results for concentration distri-
butions in the macro voids of the adsorber and within pores of the particles.
The chapter ends with a brief description of the numerical approach to simu-
late non-isothermal adsorption. Chapter 7 presents an experimental study
of the synthesis and practical application of nanozeolites-based adsorbents
in removing the commonly found toxic phenolic and metal contaminants in
many industrial wastewater effluents. This study assumes significance from
the perspective of determining the effects of physico-chemical properties of
the materials, as well as operating conditions on the removal efficiency of the
adsorbents. Chapter 8 emphasizes the treatment of the pharmaceutical com-
pound containing wastewater using a hybrid approach combining adsorp-
tion and photocatalytic reaction, rather than a single technique. Several new
antibiotic compounds have been developed in the last decade, which can
potentially enter the surface water through various channels endangering
the aquatic lives, present even at trace levels. Therefore, the remediation of
such water invariably requires a carefully designed and tested approach.
The most useful aspect of the chapter is the description of a case study of
Preface ix

treating the oxytetracycline contaminated water and toxicity tests on the

treated water. Chapter 9 takes up the most interesting but challenging aspect
of wastewater pollution and control: Can we not only treat wastewater but
also recover the waste as a useful product? Well, it can be done. The study
described in this chapter shows that although agricultural activities and food
industry over the last decade have tremendously increased the generation of
a huge volume of residues such as husks, seeds, and peel, these residues can
be reused or revalorized to produce bioadsorbents for organic and inorganic
pollutants in wastewater. The last chapter, Chapter 10, provides an industrial
perspective of adsorption applied as an efficient technique for providing
clean drinking water. The study describes the development of a water filter
based on activated carbon which is the most commonly used adsorbent mate-
rial worldwide. Besides emphasizing the roles of surface functional groups
present in the carbon substrate in removing different pollutants in water, the
study recommends the surface modifications of carbonoceous material with
a view to specifically removing toxic metals and organic contaminants from
water. The chapter illustrates the findings with the laboratory and field data
collected for water filters fabricated from the catalytic carbon.
http://taylorandfrancis.com
Editors

Prof. Jayant K. Singh is a professor in the Department of Chemical

Engineering at Indian Institute of Technology Kanpur, Kanpur, India.
Dr. Singh’s current research interest is in material modeling, self assembly,
energy storage, wetting transition, nanotribology and selective adsorption.
Dr. Singh has co-authored more than 100 peer-reviewed articles in inter-
national journals of repute. He is a recipient of prestigious awards such as
JSPS Invitation Fellowship, Alexander von Humboldt Research Fellowship,
Young Engineers of Indian National Academy of Engineering, Amar Dye
Chem Award of IIChE, BRNS Young Scientist Award, and DST-BOYSCAST
Fellowship. He is also an elected member of National Academy of Science,
India.

Prof. Nishith Verma is a professor of chemical engineering at the Indian

Institute of Technology Kanpur, India. His research interests are the develop-
ment of carbon-based materials, especially carbon nanofibers and nanopar-
ticles in adsorption, catalytic reactions, biomedical, drug delivery, sensors,
microbial fuel cells and agricultural applications. He has also developed
lattice Boltzmann method-based mathematical models for adsorption and
flow systems. Prof. Verma has published more than 100 research articles in
peer-reviewed international journals and has 8 Indian and US patents filed/
granted. Prof. Verma is an Alexander Humboldt Fellow.

xi
http://taylorandfrancis.com
Contributors

Cristina Agabo García Jianwen Jiang

University of Pablo de Olavide NUS
Seville, Spain Singapore

Zuzana Benková Anitha Kommu

Polymer Institute IIT Kanpur
Slovak Academy of Sciences India
Slovakia
Byeong-Kyu Lee
Anil Boda University of Ulsan
BARC Korea
Mumbai, India
Mridula P. Menon
Robert Chang-Tang Chang
National Ilan University
National Ilan University
Taiwan
Taiwan
Sk. Musharaf Ali
Bor-Yann Chen
BARC
National Ilan University
Mumbai, India
Taiwan

M. Natália D. S. Cordeiro Santiago Rodriguez-Perez

University of Porto University of Pablo de Olavide
Portugal Seville, Spain

Ashish Kumar Singha Deb Thi-Huong Pham

BARC University of Ulsan
Mumbai, India Korea

Vivekanand Gaur Pooja Sahu

Columbus Industries BARC
Ohio Mumbai, India

Krishna M. Gupta Jayant K. Singh

NUS IIT Kanpur
Singapore India

Gassan Hodaifa Arun Kumar Subramani

University of Pablo de Olavide National Ilan University
Seville, Spain Taiwan

xiii
xiv Contributors

Nishith Verma Qiao-Jie Yu

IIT Kanpur National Ilan University
India Taiwan

Xiao-Dan Xie Ke-Fu Zhou

National Ilan University National Ilan University
Taiwan Taiwan
1
Theory, Molecular, Mesoscopic
Simulations, and Experimental Techniques
of Aqueous Phase Adsorption

Jayant K. Singh and Nishith Verma

CONTENTS
1.1 Adsorption from Liquid Solution.................................................................2
1.2 Thermodynamics of Surface Adsorption....................................................2
1.2.1 Langmuir Isotherm............................................................................3
1.2.2 Freundlich Isotherm........................................................................... 4
1.2.3 BET (Brunauer, Emmett and Teller) Isotherm................................ 5
1.3 Computer Simulations for Adsorption Studies..........................................5
1.3.1 Molecular Simulations....................................................................... 6
1.3.2 Monte Carlo Simulations................................................................... 7
1.3.3 Molecular Dynamics (MD) Simulation...........................................8
1.3.4 Average Properties.............................................................................. 9
1.3.5 Density Profiles...................................................................................9
1.3.6 Hydrogen Bonding........................................................................... 10
1.3.7 Diffusion Coefficient........................................................................ 11
1.3.7.1 Einstein Relation................................................................ 12
1.3.7.2 Green-Kubo Relation......................................................... 12
1.3.8 Residence Time.................................................................................. 12
1.3.9 Free Energy Calculations................................................................. 13
1.3.9.1 Basic Formulation of Free Energy Calculations............ 13
1.3.9.2 Umbrella Sampling Method............................................. 14
1.3.9.3 Weighted Histogram Analysis Method (WHAM)........ 16
1.4 Mesoscopic Approach.................................................................................. 18
1.4.1 Introduction to LBM......................................................................... 20
1.4.2 D2Q9 Square Lattice......................................................................... 20
1.4.3 Model Development for the 2-D Flow of a Pure Fluid................ 21
1.4.4 Equilibrium Distribution Function................................................22
1.4.5 Boundary Conditions....................................................................... 24
1.4.6 LBM-Based Model for Adsorption in Packed Beds..................... 29

1
2 Aqueous Phase Adsorption

1.4.7 Adsorption Breakthrough Analysis...............................................30

1.4.8 Boundary Conditions....................................................................... 32
1.5 Experimental Techniques............................................................................ 32
1.5.1 Equilibrium Adsorption Loading from Flow Study................... 36
References................................................................................................................ 39

1.1 Adsorption from Liquid Solution

In Chapter 1, we briefly present the fundamentals of adsorption theory. In
addition, we provide an overview of simulation methods and experimen-
tal techniques that are commonly used to study the adsorption phenomena
from liquid solution.

1.2 Thermodynamics of Surface Adsorption

Consider a mixture of two species such that there is a phase separation into
phase α and phase β. The Gibbs-Duhem equation for the composite phase
α + phase β + interface system can be written as:

−SdT + Vdp − N 1dµ1 − N 2 dµ2 − Adγ = 0 (1.1)

where S, V, and Ni are the total entropy, volume, and number of moles of spe-
cies i in the two-phase system, respectively, and μi is the chemical potential
of component i. To maintain equilibrium between the phases, an isothermal
change in pressure must be accompanied by changes in the chemical poten-
tials that permit them to remain equal between the phases. These changes
can be described by Gibbs-Duhem equations written separately for the two
phases:

−Sα dT + V α dp − N 1α dµ1 − N 2α dµ2 = 0

(1.2)
−Sβ dT + V β dp − N 1β dµ1 − N 2β dµ2 = 0

with the phases indicated by the superscript (α or β). Alternatively, the above
equation can be written as:

(
V α − sα dT + dp − c1α dµ1 − cα2 dµ2 = 0 ) (1.3)
Vβ ( − s dT + dp − c dµ
β β
1 1 − c dµ ) = 0
β
2 2
Theory, Simulations, and Techniques of Aqueous Phase Adsorption 3

where ci is the concentration of species i in the bulk phase and s is the entropy
density. By subtracting each equation in (1.3) from equation (1.1), and divid-
ing by the area, we obtain a Gibbs-Duhem equation that amplifies the effects
of the interface:

ˆ + A1 (V − V α − V β )dp − Γ 1dµ1 − Γ 2 dµ2 − dγ = 0

− sdT (1.4)

where ŝ is the surface excess entropy. The surface excess of species i is

defined as:

(
Γ i = N i − cαi V α − ciβ V β /A ) (1.5)

At the level of detail where the interface is significant, the volumes Vα and
V are ambiguous. The value of Γi depends on the position of the Gibbs divid-
β

ing surface and the volume. Thus, an alternative approach for the calculation
of surface excess amount is also preferred. The surface excess amount Γi, for
adsorption from liquid phase can be written as

(
Γ i = N i − cilVol /A ) (1.6)

where Vol is the volume of the liquid phase up to the interface and i = 1,
2 represent the component.
For a binary system, we can write:

(
Γ 1 = N 1 − c1l Vol /A ) (1.7)

(
Γ 2 = N 2 − c2l Vol /A ) (1.8)

Thus, we can write:

Γ=
(N o
− c lVol ) (1.9)
A

where Γ = Γ 1 + Γ 2 , N o = N 1 + N 2 , c l = c1l + c2l .

Then the reduced excess amount for the component 1 is defined by elimi-
nation of Vo from the above equation.

1.2.1 Langmuir Isotherm
The correlation of one component adsorption on a solid surface is well inves-
tigated and reported for the gas phase. Several of such correlations such as
Langmuir, Freundlich, Slips, Troth, and others can easily be extended to the
liquid-phase adsorption.
4 Aqueous Phase Adsorption

FIGURE 1.1
Representation of the adsorption process, where symbol (θi) is the fraction of the surface
sites occupied. (From Lyubchik, S. et al., Comparison of the Thermodynamic Parameters
Estimation for the Adsorption Process of the Metals from Liquid Phase on Activated Carbons,
in Thermodynamics – Interaction Studies – Solids, Liquids and Gases, InTech, Rijeka, p 95–122, Ch. 4.

The Langmuir isotherm (1918) is one of the simplest models of physical

adsorption [1]. This model assumes monolayer coverage, constant binding
energy between surface and adsorbate, and no interaction among adsorbed
molecules. The Langmuir isotherm is expressed as:

K L × qmax Ce
qe = (1.10)
1 + K L Ce

where Ce is the equilibrium concentrations of the adsorptive in liquid

phase, and qe is the amount adsorbed on the adsorbent surface. Langmuir
isotherm has two adjustable parameters viz., qmax and KL, where qmax is the
maximum adsorption capacity (monolayer coverage), usually expressed in
terms of mmol of the adsorbate per (g) of adsorbent, and KL is the constant
of Langmuir isotherm. Figure 1.1 presents an illustration of monolayer cov-
erage of adsorbed species on the adsorbent, and the corresponding type of
adsorption isotherm.

1.2.2 Freundlich Isotherm
This is an empirical isotherm, which assumes that the amount adsorbed at
equilibrium has a power law dependence on the concentration of the solute
[1]. The Freundlich isotherm is expressed as:
1
qe = K F × qmaxCe n (1.11)

It may be considered to be a two-parameter isotherm, where K F and n are

the “adjustable parameters.” These parameters are calculated from a “log-log
plot” of qe versus Ce, which should be a straight line of slope 1/n and intercept
log K F. The parameters K F and 1/n are related to adsorption capacity and
adsorption efficiency, respectively.
Theory, Simulations, and Techniques of Aqueous Phase Adsorption 5

1.2.3 BET (Brunauer, Emmett and Teller) Isotherm

The Brunauer-Emmett-Teller equation (1938) considers multilayer adsorption
behavior for many systems [1,2]. Figure 1.1 presents the adsorption isotherm
and corresponding layer formation of adsorbed species on the adsorbent.
The equation is given as

K BET × qmaxCe
qe = (1.12)
(Ci − Ce ) ×  1 + ( K BET − 1) × (Ce/Ci ) 

where Ci is concentration of the solute when all layers are saturated, qmax is
the maximum amount of solute adsorbed and KBET is the parameter related
to the binding intensity for all layers. This is one of the most popular equa-
tions for determining the specific surface area of a solid.

1.3 Computer Simulations for Adsorption Studies

Theoretical studies tend to be based around simple models: aiming to reduce
the complexity of the problem but retaining the essential physics. Thus, it is
often difficult to compare theoretical predictions with experimental results.
Computer simulations have played a valuable role in bridging the gap
between theory and experiment. Computer simulations can provide exact
results for these simple models, and hence can be used as a test of theory.
Computer modeling is used to provide insight and understanding of how
complex systems behave beyond what theory and experiment could deliver
separately [3]. We may test a theory by conducting a simulation using the same
model. We may also test the model by comparing with experimental results.
Furthermore, we may also carry out simulations of certain processes or phe-
nomena on the computer that are difficult or impossible in the laboratory.
Computer simulation also provides a route to the macroscopic details (equa-
tions of state, materials properties, etc.) from the microscopic detail (atomic
masses, atomic charges, etc.). They also allow the straightforward elucidation
of detail at the microscopic scale, which can be difficult (if not impossible)
to probe from experiment. The simulations act as a bridge between micro-
scopic and macroscopic length, and time scales as shown in Figure 1.2. The
hidden detail behind bulk measurements can also be revealed. For instance,
the structure of a fluid is easily found from simulation but somewhat more
difficult from experiment. Additionally, it also provides a route to determin-
ing properties in situations out of the reach of experiment, such as high pres-
sures or temperatures. However, in all these cases, predictions of properties
are dependent on a good model of the interactions between molecules.
6 Aqueous Phase Adsorption

FIGURE 1.2
A schematic diagram of length and time scales accessible by simulation techniques.

In the studies of adsorption phenomena, computational studies can range

from quantum chemical calculations to continuum simulations. In this book,
we provide a brief description of simulation methodologies from molecular
scale to mesoscopic scale.

1.3.1 Molecular Simulations
Molecular simulations at atomistic scale can broadly be divided into two cat-
egories in terms of methods: Monte Carlo simulation and molecular dynam-
ics. These methods invariably use the statistical mechanical formalism,
which connects thermophysical properties such as pressure, energy, and
other macroscopic properties to the collection of microstates of systems of
molecules, all having in common extensive properties, also called ensemble.
A microstate of a system of molecules is a complete specification of all posi-
tions and momenta of all molecules. Most commonly, we encounter the total
energy, the total volume, and/or the total number of molecules (of one or
more species, if a mixture) as extensive properties.
Some examples of ensembles are:

• Micro-canonical ensemble
• Canonical ensemble
• Isothermal-Isobaric ensemble
• Grand-canonical ensemble.
Theory, Simulations, and Techniques of Aqueous Phase Adsorption 7

1.3.2 Monte Carlo Simulations

Monte Carlo is a computer simulation that is based on repeated random
sampling, i.e., using random numbers in scientific sampling. In general, this
method uses random numbers to solve problems that are difficult to solve
using other simple computational methods. The origin of Monte Carlo simu-
lation technique lies in the early 1940s when Fermi, Ulam, von Neumann,
Metropolis, and others used random numbers to examine problems in phys-
ics from stochastic perspective [4]. Monte Carlo simulation is used to study
a wide range of scientific areas. In Monte Carlo simulations for molecular
systems, configurations are generated using equilibrium probability distri-
bution, π, based on a statistical mechanical ensemble. For example, a typi-
cal Monte Carlo simulation uses the following steps repetitively to perform
sampling of phase space:

i. Generation of trial configuration by perturbing the original configu-

ration. For example, a randomly selected particle of the existing sys-
tem is perturbed by an amount (also referred as displacement move).
ii. The ratio of probabilities of going from a current configuration (old)
to a next configuration (new) after a trial, as per the detailed bal-
anced, is computed as:

P(old → new) π new

= (1.13)
P(new → old) π old

For a displacement move, the above ratio is exp[−(Unew − Uold)/kT],

where U, k, and T are configurational energy, Boltzmann constant and
temperature, respectively.
iii. If the trial is accepted, the new configuration is taken as the next
state in the Markov chain; otherwise the original configuration is
taken as the next state in the chain. The above is represented as:

 π 
Pacc (old → new) = min  1, new  (1.14)
 π old 

iv. The steps from i to iii are repeated for large number of steps in order
to generate large number of configurations.
v. Interested properties are collected after every few 100 or suitable
number of steps and average values are generated.

The Monte Carlo method is free from the restrictions of solving Newton’s
equation motion. Specific moves can be combined in a simulation for a
greater flexibility in sampling important configurations.
8 Aqueous Phase Adsorption

1.3.3 Molecular Dynamics (MD) Simulation

For a set of N-particles in a system of volume V, the Newtonian motion can
be expressed by two first-order differential equations as:

Pi
ri = (1.15)
mi

∂U (r N )
p i = − (1.16)
∂ri

The ri and pi are the position and momentum vectors of particle i, respec-
tively. Here, U is the potential energy which depends on the positions of all
the N-particles. In molecular dynamics simulation, we perform the integra-
tion of Newton’s equation of motion for all the particles in a system and thus
new configurations are being generated. Time averages are taken to evaluate
average properties of interest. Molecular dynamics simulations are very sim-
ilar to the real experiments. In a molecular dynamics simulations approach,
we perform the following steps:

i. Preparation of initial system: Setting up the coordinates and assign-

ing velocities of each particle of the system. It can be done either
by placing the particles on a FCC lattice or using random number
generator to place particles randomly in the simulation box. Initial
velocities are usually generated according to the Boltzmann distri-
bution for a given temperature.
ii. Force calculations: The forces on all particles at each time step, which
are needed in the integration step.
iii. Integration: There are several algorithms that are designed to inte-
grate equation of motion. The Verlet algorithm [5] is one of the sim-
plest and also usually the best to integrate the equation of motion.
The coordinate of the particle, around time t, is written in the follow-
ing form using Taylor’s expansion:

1 1
r(t + ∆t) = r(t) + v(t)∆t + f (t)∆t 2 + ∆t 3 .
r + O(∆t 4 ) + … (1.17)
2m 3!

Similarly,

1 1
r(t − ∆t) = r(t) − v(t)∆t + f (t)∆t 2 − ∆t 3 .
r + O(∆t 4 ) + … (1.18)
2m 3!
Theory, Simulations, and Techniques of Aqueous Phase Adsorption 9

Addition of the above equations results:

1
r(t + ∆t) = 2 r(t) − r(t − ∆t) + f (t)∆t 2 (1.19)
2m

Velocity of each particle can also be calculated from the above equations,
as described below:

r(t + ∆t) − r(t − ∆t)

v(t) = + O(∆t 2 ) (1.20)
2 ∆t

In another algorithm, velocity Verlet algorithm [6,7], the velocities and

positions are calculated at each time step.
The time average of any quantity calculated from the phase-space, gener-
ated using molecular dynamics simulations, is equivalent to the ensemble
average under a significant number of sampling configurations. While NVE
ensemble is a natural choice for molecular dynamic simulations, in practice we
are interested in controlling the temperature and pressure for its experimental
realization. Thus, other ensembles such as canonical (NVT) and isothermal-
isobaric (NPT), and grand canonical (μVT) ensembles are more commonly
used for real applications. To maintain a constant temperature or pressure
of the system, the equation of motion employed in the molecular dynamics
method is appropriately modified using different numerical techniques [8–10].
One of the popular molecular dynamics tools that is versatile and powerful in
simulating adsorption from aqueous phase at molecular level is LAMMPS [11].

1.3.4 Average Properties
The trajectories obtained from the molecular dynamics simulations or Monte
Carlo are used to calculate various properties of the system. The thermo-
dynamics properties are evaluated using either integration over trajectories
(MD) or using ensemble average (MC). In calculation of thermodynamical
properties, adequate sampling is required in order to minimize the errors. It
helps to minimize the fluctuations while computing structural and dynami-
cal properties of the system. The trajectories can be visualized using VMD
[12], which many is also useful in understanding the behavior and can also
act as a check against an expected behavior of the system.

1.3.5 Density Profiles
Adsorption of liquid or impurities on a solid surface can usually be described
by calculating density profiles along axis (or axes) of interest. A typical way
to calculate density profile is by dividing the system into a certain number
of bins and evaluating the number of particles accumulated in each bin at
10 Aqueous Phase Adsorption

different frames based on their coordinates. The bin density is averaged over
number of frames to obtain the density profiles along the axis of interest.

1.3.6 Hydrogen Bonding
Hydrogen bonding is a special type of dipole-dipole attraction between
molecules. It results from the attractive force between the hydrogen atoms
covalently attached to an electronegative atom (N, O, F) of a different mol-
ecule. The understanding of hydrogen bonding calculation using molecular
dynamics is well documented by Ohmine and Tanaka [13]. The hydrogen
bonding between any two water molecules are determined by the fulfill-
ment of the following criteria [14,15]:

i. Distance between the oxygen atoms of two water molecules, ROO

should be less than 3.5 Å as shown in Figure 1.3(a), which is derived
from radial distribution function of water molecules in molecular
dynamics as well as from neutron and x-ray scattering data [16].
ii. The distance between the oxygen of the acceptor molecule and the
hydrogen of the donor, ROH ≤ 2.5 (see Figure 1.3(a)). This distance is
also derived from the first minimum of the RDF of water.
iii. The angle between the vector joining the intermolecular oxygen and
O-H bond of acceptor molecule should be equal to 30°.

Figure 1.3(b) presents the hydrogen bonding formation between two water
molecules by the fulfillment of above three conditions. Using different mod-
els of water molecules, the number of hydrogen bonding differ to some extent.
Using TIP4P water model at 25° C, the average number of hydrogen bonds per
molecule was found to be 3.59 [17], however, more recent study reported the
value of 2.357 [18]. The structure and dynamics of liquid water is described
using the instantaneous hydrogen bonding. Even in equilibrated water, the
population operator of hydrogen bond fluctuates with time. The intermittent
hydrogen bond fluctuation is characterized by the correlation function:

c(t) = h(0)h(t) / h (1.21)

FIGURE 1.3
(a) Representation of hydrogen bonding criteria (not to scale) and (b) hydrogen bonding
between two water molecules.
Theory, Simulations, and Techniques of Aqueous Phase Adsorption 11

where h is the population operator of hydrogen bonds and h(t) equals to

unity if a water molecule is hydrogen bonded.

1.3.7 Diffusion Coefficient
The main advantage of MD simulation is the trajectory of particles/­molecules
of the system. Thus, it gives a route to calculate dynamical properties of the
systems, i.e., diffusion coefficients, shear and bulk viscosity, and thermal
conductivity. In this section, we discuss the computation of diffusion coef-
ficient from MD simulations.
According Fick’s law, the flux j of the diffusing species is proportional to
the negative gradient in the concentration of that species. The proportional-
ity constant, D, is referred as the diffusion coefficient.

uρ(r , t) = D  ∇ρ(r, t)  (1.22)

where ρ, u are the local density and velocity respectively which are func-
tions of position r and t. Time evolution of the density of the system is
described by:

∂ρ(r , t)
= D∇ 2 ρ(r , t) (1.23)
∂t

Using the boundary condition, ρ(r,0) = δ(r), the solution of the above equa-
tion yields an expression for ρ(r,t). Our interest is to find the displacement
of a particle in space and time. Ensemble average of displacement can be
described as:

r 2 (t) =
∫ dr[ r ρ(r,t)]
2
(1.24)

Now, the diffusion, which is displacement per unit time, can be described as:

∂ 2 ∂
∂t
r (t) =
∂t ∫ dr r ρ(r , t) = D ∫ dr  r ∇ ρ(r,t) 
2 2 2
(1.25)

Solving above equation results Einstein equation of diffusion, as described

below:

∂ r 2 (t)
= 2 dD (1.26)
∂t
12 Aqueous Phase Adsorption

Whereas D is the macroscopic transport coefficient, and d is the dimen-

sionality of the system. We describe below two different approaches for cal-
culating diffusion coefficients.

1.3.7.1 Einstein Relation
The Einstein relation is also called the mean square displacement (MSD)
relation. In this method, the mean square displacement for every particle
in the system are calculated and averaged over time. The mean square dis-
placement is plotted as a function of time. The diffusion coefficients can be
calculated using log-log plot of the MSDs as a function of time. In general,
the MSD can be expressed in power law as r 2 (t) ~ 2 dDt v, where v is the
anomaly parameter. For different values of v, the diffusion behavior can be
characterized as

i. Sub-diffusion (v < 1), commonly found in case of polymer like mac-

romolecular systems [19,20]
ii. Normal diffusion (v = 1)
iii. Super diffusion (v > 1)
iv. Ballistic diffusion (v = 2).

It is difficult to obtain all the regimes in a system; however, in Brownian

granular systems, all four regimes can be observed [21].

1.3.7.2 Green-Kubo Relation
The diffusion coefficient can also be evaluated by the Green-Kubo relation
[22,23], which is given by:

∞ N

∫ ∑ v (t)v (0)
1
D= i i dt (1.27)
3N i=1
0

The term <vi(t). vi(0)> in the Green-Kubo relation is called velocity autocor-
relation function (VACF), because it describes correlations between velocities
of tagged particle at different times along an equilibrium trajectory. For clas-
sical systems, the Einstein relationship and the Green-Kubo relationship are
strictly equivalent [23].

1.3.8 Residence Time
The residence time of molecule is an important parameter to evaluate in
order to understand the binding ability of an absorbent. It is calculated using
residence auto correlation function CR(t):
Theory, Simulations, and Techniques of Aqueous Phase Adsorption 13

∑θ (t )θ (t + t )
i=1
i 0 i 0

CR (t) = N
(1.28)

∑θ (t )θ (t )
i=1
i 0 i 0

CR (t) = A exp[−(t/τ s )] (1.29)

where θi(0) = 1 when the molecule i is found in the region of interest (could
be within the first monolayer of a surface, or within the structure of a porous
adsorbent at time t = 0). If an appended molecule continuously remains region
of interest as the time ‘t’ progresses, then θi(t) = 1; θi(t) = 0 when the molecule
exit the region of interest. The θi(t) remains equal to 0 even if the molecule
eventually returns inside the region. The residence time (τs) is evaluated by
fitting an exponential form, as shown in equation (1.29), to the CR(t) values.

1.3.9 Free Energy Calculations

Free energy is arguably the most important general concept in physical
chemistry. The free energies of molecular systems describe their tendencies
to associate and react, and thus is an important property to evaluate in order
to assess phase transition, adsorption, affinity of an ion to attach to a ligand
and so forth. Hence, developing efficient methods to evaluate free-energy
difference between two states is one of the important goals in molecular
simulation community [24,25].

1.3.9.1 Basic Formulation of Free Energy Calculations

The statistical mechanical definition of free energy is in terms of the parti-
tion function, a sum of the Boltzmann weights of all the energy levels of the
systems. However, only for the simplest model system can this free energy
be represented by an analytical function. One can write a classical analog of
the quantum mechanical partition function where the energy is viewed as a
continuous function, rather than discrete. This is likely to be good approxi-
mation in most systems involving noncovalent interactions near room tem-
perature. Unfortunately, the free energy represented in this way requires an
integration over all 3N degrees of freedom, where N = number of atoms in
the system. Thus, this is impractical in most cases. However, if one focuses
on free energy difference then it can be represented as:

GB − GA = ∆G = − RT ln e − ∆H/RT A (1.30)
14 Aqueous Phase Adsorption

where ΔH = HB-HA and < >A refers to an ensemble average over the system
represented by Hamiltonian HA. Equation (1.30) is the fundamental equation
of free energy perturbation calculations [24,25]. If systems A and B differ
in more than a trivial way, then equation (1.30) will not lead to a sensible
free energy. One can, however, generalize the problem and describe the
Hamiltonian H(λ) as equation (1.31):

H (λ ) = λ H B + (1 − λ )H A (1.31)

where λ can vary from 0 (H = HA) to 1 (H = HB). One can then generalize equa-
tion (1.30) as follows:

∆G = GB − GA = ∑ −RT ln e
λ=0
− ∆H ′/RT
A (1.32)

where ΔH´ = Hλ+Δλ-Hλ. Here, we break up the free energy calculation into
windows, each one involving a small enough interval in λ to allow the free
energy to be calculated accurately.
An alternative to free energy perturbation calculations is thermodynamic
integration [24,25], where the free energy difference between two systems
(one characterized by H = HA or λ = 0 in equation (1.31) and the other by H =
HB or λ = 1 in equation (1.31)) can be represented as:
λ =1
∂H
∆G =
∫
λ =0
∂λ
λ
dλ (1.33)

The application of equation (1.33) requires one to evaluate the ensemble

average of the derivative of the Hamiltonian with respect to λ, <∂H/∂λ>λ at
various values of λ. One can then use numerical integration methods to cal-
culate ΔG by equation (1.33).
The third commonly used method for free energy calculations is called
umbrella sampling [24,25]. This method is developed by Torrie and Valleau in
1977 and since has been one of the major approaches for performing free-energy
calculations along the whole reaction coordinates [26,27]. It is readily applied
to both molecular dynamics and Monte Carlo simulations. This can either be
aimed at in one simulation or in different simulations (windows), the distribu-
tions of which overlap. The effect of the bias potential to connect energetically
separated regions in phase space gave rise to the name umbrella sampling.

1.3.9.2 Umbrella Sampling Method

In this section, the formalism of recovering unbiased free-energy differ-
ences from biased simulations will be discussed. The bias potential wi of
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R583371.
Movie Makers, Inc.
MP25962.
Movie of the week.
LP43713.
LP43715 - LP43720.
LP43722 - LP43725.
Movie of the weekend.
LP43712 - LP43725.
Movies go West.
MP25854.
Movietone adventures.
R593744.
R593746.
R593747.
Movietone sports review.
R593732.
Movietone’s sports review.
R593745.
Moyer, Martin.
MP25954.
MP26011.
Moyer (Martin) Productions.
MP25954.
MP26011.
Mrs. B.
 MP25651.
Mrs. Liddle/bowling.
MP25644.
Much ado about nothing.
LP43952.
Muhammad Ali (Cassius Clay), champion, versus George Chuvalo,
challenger, for the heavyweight championship of the world, Maple
Leaf Gardens, Toronto, Canada, March 29, 1966.
MP25926.
Muhammed Ali versus Henry Cooper.
MP25928.
MP25934.
Muhammed Ali versus Jimmy Ellis, Houston Astrodome, July 26,
1971.
MP25932.
Muhammad Ali versus Karl Mildenberger, Frankfurt, Germany,
September 10, 1966.
MP25946.
Muhammed Ali versus Oscar Bonavena, New York, New York,
December 7, 1970.
MP25931.
Mulberry Square Productions, Inc.
LP43795.
Multiplying with fractions.
LP43748.
Munchhausen.
R584559.
Murder is a taxing affair.
LP43818.
Murder on the wild side.
LP43812.
Murder with a golden touch.
LP43828.