Article

Cite This: J. Chem. Theory Comput. 2019, 15, 1278−1292 pubs.acs.org/JCTC

Molecular Dynamics Simulation of Polarizable Gold Nanoparticles

Interacting with Sodium Citrate
Olga A. Perfilieva,† Dmitrii V. Pyshnyi,*,†,‡ and Alexander A. Lomzov*,†,‡
†
Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
‡
Novosibirsk State University, 2 Pirogova Street, Novosibirsk 630090, Russia
*
S Supporting Information

ABSTRACT: To study the structure of a citrate-capped gold

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nanoparticle and forces involved in citrate−gold interactions,

we performed a molecular dynamics simulation of a truncated-
octahedron nanoparticle containing Au(111) and Au(100)
surfaces with sodium citrate. In this paper, we employed an
approach to the modeling of interactions of a gold
nanoparticle with citrate molecules taking into account the
image charge effect in the metal. First, we built models of 6
and 14 nm nanoparticles, which can reproduce the polar-
ization effects, based on a rigid-rod gold model and the GolP-
CHARMM force field. To verify the simulation results, we analyzed density plots, radial distributions, distributions
perpendicular to Au(111) and Au(100) surfaces, the electric potential of the system, and the dynamics of citrate crown
formation. We observed formation of a stable citrate crown around the nanoparticle and detected nonuniform surface
distribution of citrate ions with the preference for Au(111) facets over Au(100) ones. Testing of the model of the citrate-capped
gold nanoparticle in a simulation at high concentrations of Na+ and Cl− ions (0.8 M) showed incorporation of chloride anions
into the citrate crown. We compared the results of citrate crown formation between polarizable and nonpolarizable gold models
and noticed a difference in the citrate distribution on the surface of the gold nanoparticle. We found that polarization effects in
the metal are involved in the mechanism of interaction of the gold nanoparticle and citrate ions. The obtained results are in
good agreement with experimental data and computer simulations from a number of other studies, which prove the validity of
the proposed model.

■ INTRODUCTION
The structure and properties of the gold nanoparticle coated
with a citrate shell (also called a crown) or other ligands have
been actively studied by different groups of researchers.1−9
Among the various procedures used in these studies, in silico
research methods play an important role.10−16 In particular,
such methods deal with the system at the nanoscale level and
represent a useful tool for identifying the mechanisms of
interaction of a citrate molecule with the surface of a gold
nanoparticle and for determining the structure of the citrate
crown around the nanoparticle. This type of simulation
requires a special approach to parametrization of the
interactions in an ensemble of molecules.
Methods of quantum chemical calculations are employed to
study the interaction of a surface with surrounding molecules
in small systems (up to several hundred atoms). For example,
ab initio Car−Parrinello molecular dynamics (MD) simulation
of an aqueous Au(111) surface has revealed orientation of the
water molecule on the atop site of gold atoms.17 Density
functional theory (DFT) calculations of adsorbate binding
energy and of interaction geometry in vacuum are often carried
out for parametrization of force fields, especially in the absence
of experimental data.18−21 Quantum mechanical calculations
enable a detailed study of a system at the atomic level, but the
computational cost for such methods is high.22,23
The classical MD approach involving different force fields
makes it possible to investigate large molecular assemblies
(millions of atoms) for long periods (up to microseconds).23
This type of system consideration and representation is
suitable for studies on large nanoparticles (larger than 10
nm), which can serve as a substrate platform for polymer
molecules such as DNA or peptides.
To analyze the interaction of a gold surface with other
molecules using the MD approach, a number of special force
fields have been developed. CHARMM-METAL24 is an
example of a force field that does not take into account the
polarization effect and is suitable for the simulation of peptide
adsorption on gold. For uncharged molecules with a small
dipole moment, the contribution of the polarization effect to
the adsorption energy is often negligible, whereas for charged
molecules, such as citrate, this effect should be taken into
account.25−27
Polarization in a metal can be examined in different ways, for
example, classically by introducing an imaginary plane behind
Received: April 16, 2018
Published: December 21, 2018

© 2018 American Chemical Society 1278 DOI: 10.1021/acs.jctc.8b00362

J. Chem. Theory Comput. 2019, 15, 1278−1292
Journal of Chemical Theory and Computation
which a charge of the opposite sign is located.27 The
capacitance−polarizability interaction model and force field
can serve as an example of another more complex approach
that was successfully applied to describe interactions of an
icosahedral gold nanoparticle (consisting of 309 atoms) and
water.28
Recently, polarization effects have been introduced into the
gold model using elements of a Drude oscillator.29 In this
model, a dummy electron is added to a positively charged core
of a gold atom forming a dipole with two opposite charges
connected by a harmonic spring. Changing of bond lengths in
the oscillator reproduces the image charge effect in the metal.
Each atom of a gold dipole also has parameters for a van der
Waals interaction. The model can be implemented with
standard force fields for simulation of biological molecules
without additional parametrization.
In the rigid-rod model, gold atoms are represented by
dipoles with a fixed bond length between charges.30,31 Dipoles
can freely rotate around the mass center of a real atom, thus
simulating polarization effects in the metal. The early force
field used with the rigid-rod model was GolP,30 which is
compatible with the OPLS-AA32 force field, developed to
model interactions of a protein with a gold surface.
Nonetheless, analysis of water molecules in this field predicts
an incorrect adsorption geometry, with the hydrogen atom
directed toward the surface; this arrangement did not match
the data of quantum mechanical calculations.17 Then, GolP-
CHARMM20,21 compatible with the CHARMM33 force field
for Au(111) and Au(100) surfaces was developed and took
into account the adsorption geometry of water and of small
organic molecules. Application of the GolP-CHARMM field is
limited to these two types of surfaces because the gold model
includes virtual sites with a specific Lennard−Jones interaction
for each type of the surface. The rigid-rod gold model has been
successfully utilized to construct Au(111) and Au(100) slabs
and to study the interactions of interface gold atoms with small
organic molecules and proteins,34−36 but nanoparticle models
of this type with Au(111) and Au(100) surfaces have not yet
been devised.
During studies on interactions of some molecules with gold
nanoparticles, it is necessary to take into consideration that
under experimentally observed conditions, gold nanoparticles
are not naked but covered by various ligands to prevent
aggregation. In the Turkevich method37 widely used for the
synthesis of gold nanoparticles, sodium citrate acts as a
stabilizing agent for gold colloids.
Investigation of citrate interaction with the gold surface is an
important field of research on nanoparticle properties.
Recently, a citrate model with bonded force field parameters
adapted for a simulation in water was developed.38 The same
group of authors also developed the GolP-CHARMM force
field, which contains the parameters for a nonbonded
interaction of citrate with Au(111) and Au(100) surfaces.20,21
The interaction of sodium citrate with the Au(111) surface in
an explicit water shell has been simulated by means of the
GolP-CHARMM force field.36 As a result, an amorphous,
multilayer organization of citrate overlayers with common
“stripe” and “islands” motifs was observed, as were more
complex structures such as loops and straight and curved
chains. It was found that Na+ ions play an important role in the
structure of overlayers and participate in the formation of
citrate bilayers on the surface of gold.
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Citrate has also been modeled with a 3 nm gold nanoparticle
having (111), (100), and (110) facets in the ReaxFF39 force
field, which takes into account events of chemical bond
formation and breakage.40 It was shown that citrate is highly
reactive with the gold surface and can form strong complexes
with gold adatoms by capturing them from the surface of the
nanoparticle. It was concluded that a fully deprotonated form
of citrate is preferable and important for the interaction with
the gold surface.
The starting point of the present study includes building of a
gold nanoparticle with polarization effects because electrostatic
interaction of the charged citrate molecule with the metal may
affect the adsorption process and energy. Another key
parameter is the nanoparticle size suitable for a comparison
with a typical nanoparticle used in experiments (usually ∼5−
20 nm in diameter [d]). Therefore, we consider a simple way
to simulate polarization in the gold model; this approach does
not dramatically change the standard MD formalization of
force fields.
Thus, the main purpose of our research was to study the
interactions of a polarizable model of a gold nanoparticle with
sodium citrate by the classical method of MD simulation. We
chose the approach proposed for formalization of the image
charge effect in gold via the rigid-rod model.30,31
The main steps of our study are listed below:
• gold nanoparticle morphology that can be realized in a
simulation force field (GolP-CHARMM) was determi-
ned;
• a rigid-rod model of a gold nanoparticle with virtual sites
for Au(111) and Au(100) surfaces was built;
• the obtained gold nanoparticle in an aqueous medium
with sodium citrate was simulated, and the results were
analyzed.
■
METHODS
MD Simulation. The MD simulations were carried out
using Gromacs41 package version 5 in the GolP-CHARMM
force field. The nanoparticle was placed in the center of the
cuboid simulation cell with the size of 13.0 × 13.0 × 13.0 nm3
for a 6 nm nanoparticle and 22.84 × 22.84 × 22.84 nm3 for a
14 nm nanoparticle. Citrate anions (fully deprotonated
C6H5O73−) were added into the system in the amount of
451 and 2756 molecules (0.34 and 0.39 M) for nanoparticles
with d of 6 and 14 nm, respectively. These values were chosen
to promote formation of a local concentrated layer around the
nanoparticles that is sufficient for assembly into a crown
structure (with 84% of the surface coverage for d = 6 nm and
100% for d = 14 nm). The percentage of coverage and the
number of citrate molecules were calculated according to data
reported by Park et al. (the density of citrate ligands was 2.8 ×
10−10 mol/cm2, which was 45% of the surface coverage).1 For
the neutralization charge of the simulation cell, sodium ions
were added into the system in an amount of three Na+ cations
per citrate molecule. The simulations were performed in
explicit water in the NVT ensemble with three-dimensional
(3D)-periodic boundary conditions by means of a Nosé
Hoover thermostat.42,43 The cutoff Verlet scheme44 was used
with particle mesh Ewald (PME)45 electrostatic summation
and was truncated at 11 Å for Lennard−Jones and Coulomb
interactions.
During the simulations, all real atoms and virtual sites were
fixed in space, and only dipole particles were free to rotate.
DOI: 10.1021/acs.jctc.8b00362
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Journal of Chemical Theory and Computation
Citrate was modeled by bonded38 and nonbonded20,21 GolP-
CHARMM force field parameters. A modified TIP3P46,47
water model and nonbonded parameters for the Na+ ion were
also taken from the GolP-CHARMM force field.
The system was first equilibrated by slow heating from 0 to
300 K with a reduced time step of 0.5 fs for 1 ns. A productive
simulation was conducted via at least 10 cycles of annealing
with a time step of 1 fs in a manner similar to that mentioned
by other authors36 testing the same model of gold. Such a
simulation method speeds up the process of cell equilibration.
The temperature of gold was maintained at 300 K, while the
rest of the system including water, citrate ions, and Na+ ions
followed a temperature cycle (300, 400, 500, 600, 500, 400,
and 300 K) of 700 ps with time checkpoints (0, 200, 225, 425,
625, 650, and 700 ps).
An additional simulation was performed with sodium citrate
and a nonpolarizable gold nanoparticle model (d = 6 nm),
which consisted only of real atoms with van der Waals
interactions. The Lennard−Jones parameters for gold were
borrowed from the CHARMM-METAL24 force field. The rest
of the conditions in the simulation, e.g., the temperature
regime, the citrate model, and the amount of citrate in the
system, were the same as those for the polarizable gold model
as described above.
For simulation of the interaction of a citrate-capped
nanoparticle with Na+ and Cl− ions, the results of crown
modeling for the polarizable nanoparticle with d = 6 nm were
employed. A snapshot of the MD trajectory obtained after a 7
ns simulation without a chloride ion served as an initial
structure for modeling. Na+ and Cl− were added to a
concentration of 0.8 M each (1323 Na+ ions and the same
number of Cl− ions) into the enlarged 14.0 × 14.0 × 14.0 nm
simulation cell. The simulation protocol was the same as that
of the modeling system without the salt. Nonbonded
interaction parameters of chloride ions with gold were
calculated according to Lorentz−Berhelot mixing rules48
σi + σj
(σij = 2 , εij = (εi*εj) ) based on GolP-CHARMM force
field parameters of Au−Au interaction. The parameters
obtained for Cl− were as follows: σ = 0.362 nm and ε =
0.9033 kJ/mol for the Au(111) surface and σ = 0.372 nm and
ε = 1.3256 kJ/mol for Au(100).
Calculation and Visualization of the Electrostatic
Potential in the System. The electric field potential was
visualized as a 3D grid with intensity of the potential at nodes
placed inside the analyzed ensemble. The magnitude of the
electrostatic potential was revealed by the concentration of
points corresponding to certain intensity.
The obtained result includes a method for taking into
consideration the periodicity of a given ensemble, a method for
optimizing the calculation and visualization of the potential
intensity, and a procedure for presenting the results in.gro
format.
The electric potential at each grid point i (Vi) is calculated as
the sum of the potentials from atomic charges of all molecules
qj
Vi = ∑ were averaged.
j,j≠i
rij (1)
where qj is the charge of the jth atom, and rij denotes the
distance from the charge of the jth atom to the ith point of the
grid in which the potential is being considered.
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Because modeling by the method of MD was carried out
under periodic conditions, it was necessary to take into
account the influence of atoms from neighboring cells during
calculation of the potential. This is especially important for the
atoms located at corners of the cell. Under 3D-periodic
conditions, each simulation cell is surrounded by its 26 copies.
For a large system, the inclusion of all atoms from the cell in
question and from neighboring cells during calculation of the
total field potential at each grid node requires large
computational resources. Because the potential from a given
charge decreases with distance as 1/r, at a given node of the
grid, the nearest charges from a neighboring cell make a greater
contribution to the intensity than do distant charges from the
same cell. To optimize the calculation process, only those
charges that fall into a cube with a side equaling to half of the
cell size and centered at the given node are taken into account
during estimation of the total electric field potential of a node;
this strategy is consistent with the Coulomb cutoff of 11 Å (see
the section MD Simulation).
The obtained values of the electric field potential at the grid
nodes were visualized by means of the points randomly
distributed near a given node and not overlapping with
neighboring nodes. Intensity of the potential was determined
via the concentration of points by means of a filter system.
Filters were the values from the absolute values of the intensity,
which determine the number of points to be placed near the
node. The system of filters forms a profile of the electric
potential intensity.
The results of calculating the 3D potential distribution were
transformed into .gro format by representing the points of the
grid as oxygen and nitrogen atoms. The sign of the potential is
indicated by different colors of the nitrogen and oxygen atoms.
When viewed in the VMD software,49 the red color
corresponds to the positive potential, and the blue color
corresponds to the negative potential. This way of
representation enables readers to visualize a given ensemble
of molecules together with the 3D potential in the VMD
software.
Computation of the Distribution of Citrate Ions
Perpendicular to the Surfaces of the Nanoparticle
and Geometrical Radial Distribution. To determine the
distribution of molecules around a nanoparticle, we considered
the position of their mass centers in the simulation cell.
For distribution perpendicular to the surfaces, we inves-
tigated the space above Au(111) and Au(100) surfaces (see
Figure S1). The number of molecules N (centers of mass)
located in the current volume was determined by going from
the surface of the nanoparticle along the normal to the plane
with specified distance step dr. The concentration of molecules
at a specific distance c(r) = N(r)/V was obtained by
normalization of the number of molecules N(r) to volume V
= dr × S, where S is an area of the surface under consideration
[Au(111) or Au(100)]. To calculate the graphs of dynamics
(Figures S15−S18), each time point was averaged over the
temperature interval 300−340 K. The graphs of 0 and 28000
ps were calculated using seven and three frames of the
trajectory, respectively; for all other time points, 10 frames
A geometrical radial distribution was computed according to
the same principles as those for the distribution perpendicular
to the surface. The concentration of molecules was determined
via the formula c(r) = N(r)/V(r), where N(r) is the number of
centers of mass dropped onto the spherical layer with thickness
DOI: 10.1021/acs.jctc.8b00362
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Journal of Chemical Theory and Computation
Figure 1. Unit cell of the face-centered cubic lattice (FCC) with additional virtual sites for {100} and {111} planes (four sites shown). Real atoms
of the lattice are represented by orange balls. Virtual sites are shown as red and blue stars for {100} and {111} planes, respectively. Examples of
{100} and {111} planes are yellow.
of distance step dr, in a thin spherical layer of volume V(r).
The starting point (zero value) for distance r was the center of
the nanoparticle.
Density map calculations were carried out by means of the
AmberTools17 package.50
■ RESULTS AND DISCUSSION
Choosing a Shape of the Gold Nanoparticle. To
construct a gold nanoparticle for simulation, it is necessary to
determine common morphological features of the nanoparticle.
Depending on the experimental conditions for obtaining
nanoparticles and their sizes, the dominant equilibrium shape
of the nanoparticle can change.51 By means of theoretical
models, researchers attempt to predict and explain the
structure of a nanoparticle under given conditions on the
basis of experimental data (e.g., direct images of a nanoparticle
obtained by microscopic techniques).52
The morphological diversity of nanoparticles can be
subdivided into two types: nanoparticles having a single face-
centered cubic (FCC) crystal lattice and twinned nano-
particles.51,53 The simple FCC shapes formed by {111} and
{100} crystal planes include a truncated octahedron,
cuboctahedron, cube, and truncated cube. Twinned nano-
particles are polycrystalline and consist of single crystal units
connected by a mirror plane. An icosahedron and decahedron
are typical examples of twinned nanoparticle shapes. A
multitwinned icosahedral nanoparticle exposes 20 surfaces
with an arrangement of atoms similar to the {111} crystal
plane. A decahedron possesses 5-fold symmetry with 10
surfaces of the {111} type. Ino and Marks decahedral
nanoparticles also include {100} facets.
Various theoretical approaches are used to determine the
equilibrial dominant form, e.g., DFT calculations, thermody-
namic, and kinetic approaches.52−62 From the thermodynamic
point of view, an equilibrium nanoparticle of a given diameter
has such a ratio of {111}, {110}, and {100} surfaces (with
different surface energies) that minimizes the total energy. For
FCC, this shape corresponds to a truncated octahedron.55,60,63
Nevertheless, if we consider the kinetic approach,53 the most
rapidly formed and kinetically stable is the icosahedral shape.
Due to the combined effects of thermodynamic and kinetic
influences, the shape of the decahedron is stabilized at greater
diameters of nanoparticles. As for the size 14 nm, which we will
consider in our simulation, it can be concluded54 that such
nanoparticles are in a transition region from the decahedral
shape to FCC shapes. The choice of truncated-octahedron
morphology can be made on the basis of the findings that this
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shape is the most thermodynamically stable52,53,64 and retains
its structure the best with increasing temperature.64
When the shape of a nanoparticle is being determined, the
ratio of {111} and {100} surfaces is an important parameter. It
is known that a nanoparticle tends to increase the presence of a
lower-energy facet {111} for its stabilization.63 According to
thermodynamic reconstruction52,60 in vacuum for the 14 nm
nanoparticle, facets {111} should constitute 90.5% of the total
surface area. In contrast, with the increasing temperature and
taking into account some kinetic factors in the model,53,54 the
theory predicts an increasing percentage of the {100} surface
area, followed by the transformation of a truncated octahedron
into a cuboctahedron. Via this approach and a phase diagram54
for a gold nanoparticle with d of 14 nm at 300 K, the
proportions of the {111} and {100} planes will be
approximately 66% and 34%, respectively.
In our simulation, we also consider a smaller nanoparticle (6
nm) sharing the morphology of a truncated octahedron as a
useful system for calculations involving moderate numbers of
atoms, although nanoparticles of such diameters may be
stabilized in an icosahedral shape.54
Building of the Gold Nanoparticle Model. To create a
gold nanoparticle, we chose a model of gold that takes into
consideration the polarization effect. The model was developed
for Au(111) and Au(100) surfaces but has not been previously
applied to construction of a gold nanoparticle. In the Gromacs
software, this gold model was used with GolP30,31 and GolP-
CHARMM force fields20,21 (based on the CHARMM force
field33) for proteins and with GolDNA-AMBER19 (based on
the AMBER force field65) for DNA and the Au(111) surface.
The special features of this model deal with representation
of gold atoms in the form of dipoles that can rotate around a
real center of an atom simulating the induced charges. This
group of atoms is responsible for electrostatic interactions. In
addition, there are virtual atoms on the surface that determine
the van der Waals interaction of gold atoms with other
molecules. Virtual sites are introduced into the model in such a
way that they lead to a correct position of an adsorbed
molecule relative to a gold atom (atop, bridge, and hollow
sites). All these features greatly complicate the model because
instead of one type of gold atom, there are several types: real
gold atoms, virtual dipoles associated with them, and virtual
sites of (111) and (100) surfaces with their own van der Waals
parameters.
The process of setting up a model is represented by the
following steps:
DOI: 10.1021/acs.jctc.8b00362
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Journal of Chemical Theory and Computation Article

Table 1. Positions of (111) Virtual Sites in the Unit Cella

(111) (111̅) (1̅1̅1) (1̅1̅1̅) (11̅1) (11̅1̅) (1̅11) (1̅11̅)
ij 1 1 4 yz ij 1 1 2 yz ij 5 5 4 yz ij 5 5 2 yz ij 1 5 4 yz ij 1 5 2 yz ij 5 1 4 yz ij 5 1 2 yz
jj ; ; zz jj ; ; zz jj ; ; zz jj ; ; zz jj ; ; zz jj ; ; zz jj ; ; zz jj ; ; zz
k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{
jij 2 ; 2 ; 2 zyz jij 2 ; 2 ; 4 zyz jij 4 ; 4 ; 2 zyz jij 4 ; 4 ; 4 zyz jij 2 ; 4 ; 2 zyz jij 2 ; 4 ; 4 zyz jij 4 ; 2 ; 2 zyz jij 4 ; 2 ; 4 zyz
j z j z j z j z j z j z j z j z
k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{
ij 1 4 1 yz ij 1 4 5 yz ij 5 2 1 yz ij 5 2 5 yz ij 1 2 1 yz ij 1 2 5 yz ij 5 4 1 yz ij 5 4 5 yz
jj ; ; zz jj ; ; zz jj ; ; zz jj ; ; zz jj ; ; zz jj ; ; zz jj ; ; zz jj ; ; zz
k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{
ij 4 1 1 yz ij 4 1 5 yz ij 2 5 1 yz ij 2 5 5 yz ij 4 5 1 yz ij 4 5 5 yz ij 2 1 1 yz ij 2 1 5 yz
jj ; ; zz jj ; ; zz jj ; ; zz jj ; ; zz jj ; ; zz jj ; ; zz jj ; ; zz jj ; ; zz
k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{ k6 6 6{
a
The header shows different types of {111} crystallographic planes. Coordinates of virtual sites in a column belong to the corresponding plane
(unit cell size is 1 × 1 × 1).

• construction and multiplication of the unit cell (with real
atoms and virtual sites) to form a cubic crystal of the
required size;
• obtaining a nanoparticle from a crystal by cutting off
excess atoms with eight planes (111) and then six planes
(100) and determination of surfaces Au(111) and
Au(100) and types of gold atoms for surfaces;
• construction of the final model of the nanoparticle by
specifying it in 3D geometrical space, addition of virtual
atomic dipoles to real gold atoms, and preparation of
files for MD simulations.
Construction of the Unit Cell and Its Multiplication. The
cubic crystal from which the nanoparticle will be derived can
be considered a set of points in 3D space with a definite
position. This set of points can be described by a 3D array of
(nx + 1) × (ny + 1) × (nz + 1) size, where nx, ny, and nz are
numbers of unit cell blocks along the x-, y-, and z-axes.
An elementary cell can also be initiated as a 3D array, which
in turn can be considered geometrically analogous to an
elementary FCC unit cell. Virtual sites for all the {100} and
{111} planes were added to the real atoms of the unit cell
(Figure 1). Virtual sites for {100} surfaces were set in the
middle of the cube edges. For the {111} surface, 4 × 8 virtual
site points were defined as centers of triangles on the
corresponding plane. If we have a unit cell with the side
equal to 1, then the coordinates of virtual atoms for {100} are
as follows: (0.5; 0; 0), (0; 0.5; 0), (1; 0.5; 0), (0.5; 1; 0), (1; 0;
0.5), (1; 1; 0.5), (0; 0; 0.5), (0; 1; 0.5), (0.5; 0; 1), (0; 0.5; 1),
(1; 0.5; 1), and (0.5; 1; 1). Taking into account the
denominator of every virtual site (111) and (100) inside the
unit cell, it is reasonable to represent each elementary cell in
the form of a 6 × 6 × 6 3D-array (du = 6) in accordance with
the position of virtual sites (see Table 1).
According to the proposed structural organization, the unit
cell can be easily extended to a cuboid crystal of any size. By
multiplying a unit cell, a researcher can create a large cubic
crystal (nx = ny = nz = n) of (du*n + 1)3 size in the form of a
3D array. Instead of a continuous list of atoms with
coordinates, the array can be used to describe the crystal
structure. The array contains only numbers that denote the
types of atoms. To label a real atom in the array, the number
“2” was employed, and virtual atoms for {100} and {111}
planes were represented by numbers “5” and “7”, respectively.
The array initialization consisted of filling it out with zeros
(“0”), which means that there was no atom in any unit cell
node. If we denote the array as [a], then each element of the
array is designated as a(i,j,k). The maximum number of
elements in each dimension of the array is (6 × n) + 1. The
array can be considered a 3D grid of an unknown geometric
scale size with real or virtual atoms that can be located in its
node. On the basis of visual representation of a unit cell, each
atom is exposed in the array. This method of data organization
is effective and visually representative for solving the problem
of nanoparticle construction. At a later stage, the array can be
transformed into a geometric structure according to the lattice
parameters of a gold crystal unit cell.
Obtaining a Nanoparticle from a Cubic Crystal and
Determining the Surfaces. The next step was to cut off
redundant atoms in the cube with planes to produce the
truncated-octahedron geometry. For this purpose, we analyzed
an atom’s position relative to the planes of the nanoparticle
surface. The equations for all 14 planes (eight planes of the
{111} type and six planes of the {100} type) for the truncated
octahedron should be defined (see Figure 2 and Supporting
Information, section “Symmetric equation for {111} and {100}
planes”). The diameter d and a ratio of total (111) and (100)
surface areas (SΣ{111}:SΣ{100}) can be used to identify the
positions of the planes when building a nanoparticle model.
For cutting off excess atoms, the cube was assumed to be
placed in a Cartesian coordinate system with the origin in the
Figure 2. Geometry of the nanoparticle obtained from the cube
crystal (thin black lines). Cutting planes {111} (thick black lines)
form an octahedron in the center of the cube. The truncated
octahedron is obtained by removing excess atoms by means of {100}
planes (pink lines). Changing the cutting position of {100} planes
relative to the center of the cube results in a different ratio of (111)
and (100) surface areas and can lead to different shapes of the
nanoparticle (an octahedron, truncated octahedron, cuboctahedron,
or cube).

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center of the cube. Each element of the array a(i,j,k) was
centered by shifting all coordinates by half of the cube side (3
× n) to use a symmetric equation for {111} and {100} planes.
An octahedron was obtained from the cube by changing the
array of elements according to their positions relative to eight
planes {111}. For the selected plane and each element of array
[a], the status of the point in the cube was redetermined: if
point a(i,j,k) was beyond plane {111} forming an octahedron,
then a(i,j,k) was redefined by zeros (“0”). Then the parameter
of {100} equations (see Supporting Information, section
“Symmetric equation for {111} and {100} planes”) determines
at what position the {100} planes are settled and enables
precise cutting of excess atoms. Thus, varying the ratio of
(100) and (111) planes, one can obtain nanoparticles of
different shapes (an octahedron, truncated octahedron,
cuboctahedron, truncated cube, or cube).
The next step was to detect the surface in the nanoparticle
model. A surface of the nanoparticle was considered for each
plane and nonzero element of array [a]. Elements in an array
that belong to cutting planes also lie on the surface of the
nanoparticle. We define these elements as surface atoms and
change the status of an element in array [a] according to the
plane type: {111} or {100}. For example, instead of values “2”,
“5”, and “7” in the array, we inserted others: “3” and “37” for
the real and virtual atom of surface (111), respectively, and “4”
and “47” for the real and virtual surface atoms of (100). The
usage of different numbers for different surfaces enabled us to
give atoms of the surface their own interaction parameter if
necessary.
After that, array [a] containing zeros where there are no
nanoparticle atoms and containing numbers where the atoms
are present was subjected to the following modification:
internal virtual atoms were deleted from the array (in our case
they are denoted by the values “5” and “7”) by setting them to
“0”.
Making of a Geometrical Space Model with a Unique
Topology Taking into Account Polarization Effects. The
information from 3D array [a] (containing representation of
nanoparticles in the form of zeros and numbers in space
coordinates (i,j,k) of array [a]) had to be transformed into 3D
geometric coordinates (x,y,z) and into certain types of gold
atoms used in the rigid-rod gold model.20,30,31
The real atoms and virtual sites of a (111) surface indicated
by values “3” and “37” of the array become AUS and AUI atom
types of gold, respectively, in the model. For a (100) surface,
the real atoms “4” and virtual sites “47” should be redefined as
AUSS and AUII, respectively. All internal real atoms “2” were
renamed to the AUB type. Each type of gold atom had its own
mass and charge according to the rigid-rod model, which is
useful for making system topology files.20,30,31
A fixed distance between elements of the array [a] 3D grid
was denoted as the scale factor (sf) variable
us
sf =
du (2)
where us = 0.40782 nm is a unit cell size parameter of the Au
lattice,66 and du = 6 is the number of unit cell partitions (see
Construction of the unit cell and its multiplication)
Using sf as the scale factor of the grid, we were able to
calculate Cartesian coordinates of all real gold atoms and
virtual sites. If a(i,j,k) is an element of array [a], then x = i × sf,
y = j × sf, and z = k × sf.
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Nonetheless, array [a] did not contain dipoles. Dipoles were
added to the model during determination of the Cartesian
coordinates of atoms. Atoms AUC with the charge 0.3e were
added to each real atom at the distance of 0.07 nm along the x-
axis to build a gold dipole in accordance with the rigid-rod
model of gold.20,30,31 The rigid-rod dipole with the AUC atom
was fixed in the topology of the system to take into account the
polarization effect during simulation. Topology of the system
also contained information about charges and masses of
different gold atom types.
Finally, output files were converted to such a format that
enables using them in the simulation of the nanoparticle in the
Gromacs package: a .gro file with coordinates; a file of the
molecule topology (.itp) with correct atom types, charges,
masses, and dipole constraints; and an index file (.ndx) in
which some atoms that had to be fixed during the simulation
were listed.
As a result, we built the nanoparticle with surfaces (111) and
(100) for which the surface atoms were defined: virtual sites
responsible for short van der Waals interactions [white for
(111) and red for (100)] and the real atoms with dipoles [gold
for (111) and blue for (100)] responsible for electrostatic
interactions. Inside the nanoparticle there were only real atoms
with dipoles. Figure 3 depicts the typical structure of the
truncated-octahedron gold nanoparticle.
Figure 3. Illustration of the typical structure of the truncated
octahedron nanoparticle model (d = 3 nm). Facets, edges, and
vertices of the nanoparticle are shown. Colors represent different
types of gold atoms: white and red are (111) and (100) virtual sites,
whereas blue and gold are real atoms. Dipole atoms are not shown.
Two gold nanoparticle models with d = 6 and 14 nm and the
surface ratio SΣ{111}:SΣ{100} of 66%:34% were constructed for
simulation. Because the truncated-octahedron nanoparticle is
not spherical, we defined d of the nanoparticle as a distance
between two opposite (100) planes. For simulation stability,
the vertex atoms were removed (see Supporting Information,
section “Preparing the nanoparticle system for simulation”).
Given that our attention was focused on binding to the
metal surface, and Au(111) and Au(100) facets occupy most
of the nanoparticle interface, we did not consider in detail van
der Waals interactions at the edges and vertices. In GolP-
CHARMM,20,21 such parameters for corners are absent.
Perhaps for a more careful analysis of the effects of edges
and vertices, these interactions should be parametrized
separately. In principle, the proposed algorithm of nanoparticle
construction makes it possible to redefine the types of gold
atoms for edges and give them special values if necessary.
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Figure 4. Dynamics of radial distributions of citrate (A), Na+ ions (B), and water (C) for the nanoparticle of d = 6 nm. The 21 ns trajectory (with a
time step of 200 ps, and a radial distance step of 0.1 nm) was smoothed using a moving average of five time points. The position of the origin of the
coordinates is at the center of the nanoparticle.

Figure 5. Dynamics of radial distributions of citrate (A), Na+ ions (B), and water (C) for the nanoparticle of d = 14 nm. The 28 ns trajectory (with
a time step of 200 ps and a radial distance step of 0.1 nm) was smoothed using a moving average of five time points. The position of the origin of
the coordinates is at the center of the nanoparticle.

Figure 6. Final snapshot of citrate crown formation after 28 and 21 ns simulations of gold nanoparticles of d = 14 nm (A) and d = 6 nm (B),
respectively. Atoms are colored according to elements: red corresponds to oxygen, green to carbon, white to hydrogen, ochre to real gold atoms,
yellow to virtual gold sites, and blue to sodium ions. Water molecules and gold dipoles are not shown.

Simulation of Gold Nanoparticles with Sodium
Citrate. The simulation of gold nanoparticles with d = 6
and 14 nm in an explicit water shell with sodium citrate was
performed for 21 and 28 ns, respectively. Formation of a stable
sodium citrate coverage was observed during the simulation for
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both 6 and 14 nm nanoparticles. This finding can be easily
illustrated by the analysis of radial geometrical distribution for
different molecules (Figures 4 and 5). The analysis of radial
distribution dynamics for citrate and sodium ions reveals the
formation of narrowing peaks around the nanoparticle. The
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maxima of peaks reach a plateau at the same time for citrate

and sodium ions; this situation corresponds to the formation of
a stable sodium citrate crown. It formed faster for the 6 nm
nanoparticle (after ∼10 ns) and took twice the time for the 14
nm nanoparticle (∼20 ns); these data are consistent with the
size of the analyzed systems. The maxima and standard
deviation of the citrate and sodium ions radial distributions
averaged over the last 3 ns of the simulation were the same: 4.3
± 0.45 nm and 8.6 ± 0.85 nm from the center of the small and
big nanoparticle, respectively (see also Supporting Informa-
tion, section “The estimation of citrate crown thickness”).
Dynamics of water molecules along the MD trajectory
indicated a replacement of water around the nanoparticle by
citrate and sodium ions (Figures 4C and 5C). The water radial
distribution curve for the small nanoparticle consists of a peak,
then a valley, followed by an increase to the plateau. The depth
of the valley correlated with the growth of ion distribution
peaks with time. A similar time trend was observed for the big
nanoparticle, but the first peak of water was absent due to the
extended surface of the nanoparticle on radial distribution
graphs (see Supporting Information section “The estimation of
citrate crown thickness”). The presence of water near the
surface of both nanoparticles was confirmed by density maps
(see Figure 8).
Snapshots of final frames for both nanoparticles are
presented in Figure 6. Almost all citrate ions were involved
in the formation of the shell around the nanoparticle at the end
of the simulation, thus indicating that the process of crown
formation ran successfully (100% of the initial citrate amount
was in the crown for d = 6 nm and 93% for d = 14 nm).
In general, we can conclude that not all the nanoparticle
surface is covered by citrate, thus resulting in heterogeneity of
the citrate crown.1,3 Citrate is organized as a multilayered shell Figure 7. A) An average normalized distribution of citrate mass
that is consistent with the experimentally estimated thickness centers perpendicular to the surface: for the nanoparticle with d = 6
of citrate coverage1 and a study on high-resolution microscopic nm (solid curves) and for the 14 nm nanoparticle (dashed curves).
images of nanoparticles.3 Blue and red curves denote Au(111) and Au(100) surfaces,
The overall distribution of citrate ions above the nano- respectively. The graph distance step is 0.1 nm, and the position of
zero is at the surface level. Typical structures of citrate overlayers
particle surface has a nontrivial structure (see Figures 7B−E
above the surface of Au (100) for d = 14 nm (B) and for d = 6 nm
and S3−S10 for more details). Nevertheless, in the (D) and Au(111) for d = 14 nm (C) and for d = 6 nm (E). Citrate is
composition of the crown, readers can see motifs of citrate represented by blue lines, and red balls indicate centers of mass of
corresponding to simulation data obtained by Wright et al. for citrate ions.
a polarizable Au(111) surface: linear and branched chains and
bilayers connected through Na+ ions.36 In the same paper,
those authors identified three adsorption states of citrate in the noticed a large so-called “third layer”, which accounted for an
amorphous overlayers: “directly adsorbed” citrate had close asymmetrical form of distribution. According to our data, the
van der Waals contacts with gold (up to 5 Å from the surface), third layer is diffuse and merges with the previous layer, in
“indirectly adsorbed” formed a bilayer through a sodium ion agreement with complex 3D structural organization of citrate
with adsorbed species (approximately 5−8 Å), and the “third ions (see Figures S3−S10). Averaged distributions above the
layer”. Lee et al. obtained a clear-cut image of citrate layers Au(100) surface reveal a significant difference from Au(111)
around a 10 nm nanoparticle by transmission electron because of a decreased number of adsorbed citrate ions and a
microscopy techniques and also concluded that the citrate more extended diffuse layer. The analysis of the visual model of
shell around the 10 nm nanoparticle consists of 2−3 layers citrate overlayers on the Au(100) surface revealed that in a
with the estimated distance between them equal to 3−3.5 Å.3 typical case, citrate ions hung over the middle part of the
The final result on citrate distribution curves perpendicular surface without binding to it. On average, citrates were closer
to the surface of the nanoparticle indicates a layered structure to the Au(100) surface of the 14 nm nanoparticle and had a
of the citrate crown too (see Figure 7A). The graph is averaged greater number of direct contacts with the surface area.
over all eight Au(111) and all six Au(100) facets. The Moreover, in the case of the 14 nm nanoparticle, some surfaces
distributions of citrate ions above Au(111) look similar Au(100) (namely 01̅0) were populated by citrate ions (see
between 6 and 14 nm nanoparticles. The first peak at a Figures S9 and S10).
distance of 0.5 nm from the surface can be attributed to the Higher magnitude of the distribution perpendicular to the
directly adsorbed citrate layer. The next high-magnitude point Au(111) surface as compared to the Au(100) surface (Figure
appears at 0.7 nm which probably corresponds to indirectly 7A) means a preference of the citrate shell for Au(111), in line
adsorbed citrates according to reference data.36 We also with the data reported by Park and coauthors.1 In that paper, a
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model of a protonated citrate form (H2Citrate−) was analyzed citrate crown and compared it with the values from radial
on Au(111), Au(100), and Au(110) surfaces to fit distribution graphs (see Supporting Information, section “The
experimental results including microscopy images of citrate estimation of citrate crown thickness” for details). The overall
layers. It was concluded that the preference for Au(111) is due result of 1.0−1.2 nm is close to experimentally measured values
to the possible binding of the terminal carboxyl group of citrate of 0.6−1.2 nm.1,3
to the bridge site of the Au(111) surface. On the other hand, To detail the localization of different molecules and atoms in
according to the arrangement of gold atoms on different the simulation cells, an analysis of the density distribution was
surfaces, formation of a citrate network is possible on both performed next. For both nanoparticles (6 and 14 nm), the
Au(100) and Au(111) surfaces in contrast to the Au(110) picture looks very similar. According to our results, the citrate
surface.1 ions concentrate mainly near nanoparticle edges and vertices,
Differential affinity to facets of a gold nanoparticle has also as proposed by Park et al.1 on the basis of measurements of
been demonstrated for other capping ligands.10−13 It is well- citrate shell thickness (see Figure 8A). Sodium ions are tightly
known that surfactant cetyltrimethylammonium bromide bound to the negatively charged citrate ions. The arrangement
(CTAB) has uneven density at side and end surfaces of a of Na+ ions in the structure (Figure 8A) indicates their major
gold nanorod. MD simulations showed that structural participation in the assembling and stabilization of the crown,
organization of CTAB on the Au(111) surface resulted in including the possibility of formation of citrate motifs. The
more open water−ion channels which provided additional analysis of citrate ion orientations relative to the gold surface
transport of growth components to nanorod ends.10−12 revealed a preferential interaction of CH2 groups with gold
Accordingly, elongation of a gold nanorod is probably atoms. Our results match the adsorption geometry of citrate on
associated with heterogeneity of surface coverage, namely a Au(111) surface reported by Wright et al.,36 because we
with high density of CTAB at the side facets ({100}, {110}) study the same model of citrate (Cit3− with optimized
and lower binding efficiency to the end facets of the {111} parameters for an aqueous medium38), the rigid-rod model
type. of polarization in gold,30,31 and the same GolP-CHARMM
We then used the distribution perpendicular to the surface force field.20,21
to estimate the number of citrate molecules directly adsorbed Water molecule density maps calculated during the last 7 ns
on the surface of a nanoparticle. The criterion for evaluation of of 28 ns MD trajectories uncovered their strong interaction
citrate molecules in close contact with the surface was the and specific orientation near the gold surfaces (Figure 8B).
distance on distribution graphs less than or equal to 0.5 nm. The water density map outlines the contours of a nanoparticle
Similar geometric principles were applied in calculations for surface, most sharply for the Au(100) surfaces (Figure 8B).
citrate molecules on the Au(111) surface.36 Table 2 shows that Detailed consideration of the water oxygen density map with
the gold surfaces showed a preferential orientation of water
Table 2. Analysis of Direct Contacts of Citrate Ions with the molecules relative to the gold atoms. For the Au(111) surface,
Surface of a Nanoparticle from the Distribution the plane of water molecules was preferentially parallel to the
Perpendicular to the Surface of the Nanoparticle for the gold surface (see Figure S19B and S19D). In the case of the
Last Three Frames of the MD Trajectory (see Methods)a Au(100) surface, parallel and, less likely, perpendicular
6 nm 14 nm
orientations were observed (see Figures 8C, S19A, and
S19C). The orientation of water on different surfaces and
surface type {111} {100} total {111} {100} total the preference for Au(100) over Au(111) are in agreement
average number 21 1 22 142 14 156 with quantum chemical calculations.20,67 The presence of more
of directly ad-
sorbed mole- tightly interacting water may influence the binding of citrate to
cules the Au(100) surface in comparison with Au(111). It can make
average number 159 94 253 1404 279 1683 an additional contribution to the predominant adsorption of
of molecules citrate on the Au(111) surface. In addition, water is most
above surface
number of mole- 451 451 451 2756 2756 2756
tightly interacting with nanoparticle edges via the oxygen atom
cules in cell without preferential orientation of the hydrogens. We propose
% of direct con- 4.7% 0.2% 4.9% 5.2% 0.5% 5.7% that the orientation of water on edges of a nanoparticle
tacts with sur- originates from tight interactions of the positively charged
face
% of analyzed 35.3% 20.8% 56.1% 51.0% 10.1% 61.1%
dipole atoms AUC with a negatively charged O atom (see
molecules below).
a
The molecule is regarded as directly adsorbed if the distance In summary, as a result of simulation, a structure of the
between a citrate mass center and gold atoms is less than or equal to citrate crown around a gold nanoparticle with d = 6 nm or d =
0.5 nm. 14 nm was successfully formed. We characterized the final
citrate distribution, dynamics of its formation, and final citrate
distribution for both nanoparticles. The main features of citrate
only ∼5% of citrate molecules in the simulation cell were coverage (such as heterogeneity, the presence of free gold
located directly on the surface of the 6 and 14 nm surfaces, and the thickness) were consistent with experimental
nanoparticles. Most citrate molecules adsorb indirectly on results.
the surface through Na+ ions.36 The percentage of citrate Analysis of the Electrostatic-Potential Distribution.
molecules being analyzed above the surface was ∼60% for both The resulting distribution of the citrate crown around a gold
nanoparticles (see Figure S1). The rest of the citrate molecules nanoparticle is difficult to explain without consideration of the
were associated with the edge volume of each nanoparticle. forces governing the interaction between a metal nanoparticle
To complete the analysis of the distribution perpendicular to and surrounding molecules. It seems that electrostatic forces
the surface of a nanoparticle, we estimated the thickness of the arising from polarization effects in the nanoparticle model
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Figure 8. Density maps of different atoms in systems along the last 7 ns of the MD trajectory: A) citrate O carboxyl atom (red) and Na+ ions (blue)
for the nanoparticle of d = 14 nm; B) a water oxygen atom (O) for the nanoparticle of d = 14 nm; C) a water oxygen atom (green) and water
hydrogen atoms (red) above Au(100) for the nanoparticle of d = 6 nm. Real gold atoms are shown as yellow spheres.

Figure 9. Electric potential of a gold nanoparticle of d = 14 nm in vacuum (A) and in aqueous media: with only water molecules (B) or in the
presence of citrate (C). The negative potential is blue, and the positive potential is red.

could have a considerable influence on a charged citrate
molecule during the simulation.
To reveal the possible mechanism behind the crown
formation process, intensity of the electric potential was
analyzed for the gold nanoparticles in different environments.
We compared the electrostatic field potentials of the 14 nm
gold nanoparticle between vacuum, water, and the citrate-
capped model system simulated in the periodic cuboid cell.
The electrostatic potential of the nanoparticle was visualized in
all cases as described in Methods.
In vacuum, the nanoparticle had no distinguishable charge
distribution profile at the surface or corners (Figure 9A). The
analysis of the potential of a gold nanoparticle in a water box
revealed the development of heterogeneity. The Au(100)
surface carried a stronger negative potential above the surface
than Au(111) did (Figure 9B). To compensate the potential
near the uncharged nanoparticle, the field potential near the
edges became positive. When a nanoparticle from the system
with sodium citrate was evaluated (Figure 9C), a similar
potential distribution was observed: the nanoparticle edges
acquired a positive charge, while the surfaces became
negatively charged with higher magnitude for {100} as
compared to {111}. This finding can probably explain the
origin of citrate concentration near the edges of a nanoparticle.
Because water density maps (Figure 9B) uncovered the
presence of water molecules near surfaces and edges of a
citrate-capped nanoparticle and a possibility of parallel water
orientation near Au(100) (Figures 8C and S19), we assumed
that these data are in agreement with the electrostatic potential
distribution. We believe that small water molecules could get
close to more open atoms at the edges and vertices and induce
a positive charge at these sites under the influence of the
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negatively charged oxygen atom of water. After that, gold
dipoles are oriented according to the geometry of a
nanoparticle and affect water adsorption on different surfaces.
Nevertheless, it is worth mentioning that citrate forms the
crown structure through sodium ions; therefore, more complex
electrostatic interactions with the surface are possible. In
addition, the arrangement of gold atoms on the surface can
affect the binding to different surfaces of the nanoparticle via
van der Waals forces.
On the basis of all these results, we can propose a
mechanism of formation of a nonisotropic citrate crown near
a nanoparticle. First, the closest water molecules cause
redistribution of gold nanoparticle dipoles. Then, the
negatively charged citrate ions get attracted to the positively
charged edges through the long-range electrostatic interactions
and form a network around the nanoparticle. After citrate
reaches the surface of the nanoparticle, the van der Waals
interactions orient the molecule on the surface in addition to
electrostatic forces. It can be assumed in the first
approximation that citrate prefers to interact with the
Au(111) surface over Au(100) owing to a weaker negative
field above Au(111).
Similar observations related to the presence of a positive
electrostatic potential on nanoparticle corners with a low
coordination number have been obtained for gold and
platinum clusters.68 This observation explains the high catalytic
activity of these sites toward Lewis bases. It seems that the
nanoparticle morphology itself determines the charge dis-
tribution and offers an additional opportunity for electrostatic
interactions with the surrounding molecules.
Comparison of Simulation Results between the
Polarizable and Nonpolarizable Model of a Gold
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Figure 10. A) The simulation results on the 6 nm citrate-capped gold nanoparticle interacting with NaCl. Na+ and Cl− ions are not depicted for
clarity. The arrow marks the place where a big group of citrate molecules lost contact with the crown. B) The last frame of radial distribution graphs
for citrate (CIT) in a system with and without NaCl (red and blue curves, respectively). The radial distance step is 0.1 nm, and the position of zero
is at the center of the nanoparticle.
Nanoparticle. To clarify the involvement of the polarization
effect in the process of citrate crown formation, we performed
simulation of the nonpolarizable model of a gold nanoparticle
(d = 6 nm) with sodium citrate. When only van der Waals
interactions with gold were considered, the citrate crown also
completely formed after 21 ns of the simulation (Figure S21A).
Moreover, the coverage had a heterogeneous multilayer
structure with the presence of naked gold surfaces as in the
case of the polarizable nanoparticle model. In contrast, the
patterns of arrangement of citrate molecules above the surface
of the nanoparticle were significantly different.
The main difference, which is clearly seen in the distribution
graphs perpendicular to the surface of a nanoparticle, is the
number of close van der Waals contacts with the gold surface
(32% of all citrate molecules in the case of the nonpolarizable
model versus 5% in the case of the polarizable model; see
Table S1, Figure S21C, and Table 2). We can propose a
possible explanation of these results on the basis of
electrostatic-potential analysis of the polarizable gold nano-
particle (see above). Inclusion of gold dipoles in the
nanoparticle model caused changes in the charge distribution,
with the negative field potential being on the surfaces and the
positive field potential near edges and vertices of the
nanoparticle. During the process of crown formation,
negatively charged citrate is affected by repulsive forces from
a surface having a negative electrostatic field in the model with
polarization. On the other hand, in the simulation of the
nonpolarizable gold model, a citrate molecule could easily bind
to the center of nanoparticle facets, thereby resulting in an
increasing number of close van der Waals contacts with the
gold surface.
Another feature of the simulation of the nonpolarizable
model of gold is comparable affinity of citrate for both types of
nanoparticle surfaces with no significant preference for
Au(111) (see Figure S21B−D). It should be noted that the
simulation was conducted under conditions of periodically
rising temperature, which increased the number of collision
events between citrate molecules and the gold surface.
Nonetheless, in the case of a nanoparticle with polarization,
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especially the small nanoparticle (d = 6 nm), the Au(100)
surface area was virtually unpopulated by citrate. We assume
that the negative electrostatic field above Au(100) in the
polarizable gold model strongly hinders the efficiency of
landing on the Au(100) surface of the nanoparticle.
The orientations of citrate with respect to the surface of the
polarizable and nonpolarizable gold model were similar, with
CH2 groups being preferentially exposed to the nanoparticle
surface, and the COOH group pointed away. Apparently, this
binding mode of citrate facilitated the assembly of “linear
chains”, “bilayers”, and “island” structural motifs, which have
been described for a polarizable Au(111) surface.36
In summary, a citrate crown was formed in both cases (in
the simulation with and without the image charge effect in the
metal). Nevertheless, the necessity of including the polar-
ization effects in the nanoparticle model is based on theoretical
principles because citrate is a charged molecule (see
Introduction).
Testing of the Citrate-Capped Nanoparticle Model
with Sodium Chloride. One of methods for testing and
studying gold nanoparticles is salt-induced aggregation. It is
known that at a high salt concentration, gold nanoparticles
aggregate with a visible color change of the solution from red
to blue.69 The aggregation mechanism is often associated with
the removal of the negatively charged citrate crown from a
nanoparticle under the influence of electrostatic forces and
uncovering of the hydrophobic gold surface for van der Waals
interactions with the surface of another nanoparticle.70
To study the suitability of the newly developed gold model
for investigation of nanoparticle properties, we carried out a
simulation of the citrate-capped nanoparticle of d = 6 with ions
Na+ and Cl− at a concentration of 0.8 M for 35 ns. We chose a
7 ns snapshot of the MD trajectory as a starting point of the
simulation. This snapshot corresponds to 95% of citrate ions
located near the nanoparticle when the formation of the crown
is clearly detectable but is not fully completed. This choice was
governed by the necessity of decreasing the simulation time to
observe possible citrate shell reorganization.
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Figure 11. A) The density map of Cl− (yellow) and citrate O carboxyl atom (cyan) with the nanoparticle of d = 6 nm along the last 7 ns of the MD
trajectory. B) Radial distribution of the last trajectory frame for citrate (CIT: blue curve), Cl− (CL: red curve), and Na+ ions (NA: yellow curve).
The radial distance step is 0.1 nm, and the position of zero is at the center of the nanoparticle.
During the simulation, we observed numerous changes in
the structure of the citrate crown. Typical processes along the
MD trajectory were as follows: repeating rearrangement of the
structure, detachment of a small number of citrate ions from
the surface, and clustering of citrates into new groups
(compare Figure S22A and S22B). After 32 ns, a large group
of citrate ions (28) separated from the shell (Figure 10A). In
the absence of NaCl, we never observed the detachment of
citrate clusters of such size from the crown during the
simulation.
Although rearrangement of the crown clearly takes place in
the structure along the trajectory, we cannot make a firm
conclusion about the radical changes in the thickness of the
crown during the simulation from the radial distribution
dynamics (Figures 10B and S23). Analysis of density maps
suggests that Cl− ions interacted with the citrate shell and got
incorporated into the crown (Figure 11A). Moreover,
localization of chloride ions at the edges of the nanoparticle
is detectable. We assume that this phenomenon originated
from a tight interaction of the positively charged dipole atoms
(AUC) with the negatively charged chloride ion, which has
smaller size and higher mobility than the citrate ion does. It
can be concluded from radial distribution graphs (Figures 11B
and S23) that sodium and chloride ions reach the same
plateau, which corresponds to the same bulk concentrations of
ions in solution.
As a result, it can be concluded that during the 35 ns
simulation, we did not detect the complete removal of the
citrate crown. Even though Cl− ions are incorporated into the
crown, Na+ ions are still located there and, apparently,
maintain its structure (Figure S22D). Nevertheless, the results
indicate that there are changes in the structure of the crown
under the influence of NaCl.
In summary, gold nanoparticles hold promise for various
chemical and physical interactions and cause adsorption of a
molecule from the surrounding medium. Besides, the presence
of surfaces with different arrangements of atoms as well as
specific sites with low coordination such as edges and vertices
further complicates the modes of binding to a nanoparticle. It
seems that depending on their functional groups and charges,
molecules can interact with different regions of the nano-
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particle. A study on displacement of oligonucleotides (non-
covalently attached to a gold nanoparticle) by thiols points to
the existence of various regimes involving only partial
displacement of DNA from the surface of a gold nanoparticle
by high-molecular-weight thiols and complete removal of DNA
by low-molecular-weight thiols.71 A layer-by-layer approach
applied to obtain the gold nanoparticles with multilayer
coverage (consisting of positively and negatively charged
ligands) indicates the possibility of mixing the layers and
formation of a shell with heterogeneous mosaic structure.72
The existence of selective surface-capping agents63,73 as well as
production of nanostar structures during nanoparticle over-
growth74,75 also confirms the nontrivial nature of binding to
the surfaces and edges of a nanoparticle. The MD method can
serve as a useful tool for investigating the interactions with
metal nanoparticles. Analysis of our simulation results
uncovered formation of a citrate crown around the gold
nanoparticle. This finding is in good agreement with
experimental data on its thickness and structure.
■ CONCLUSIONS
We developed a gold nanoparticle model with the polarization
effect using the original method of unit cell initiation, cutting a
nanoparticle out of a crystal cube, and detecting the surfaces
and different types of gold atoms. As a result of modeling of
the gold nanoparticle with sodium citrate, a citrate-capped gold
nanoparticle model was obtained for the first time. The model
was verified according to the literature data. The model
reproduces such important properties as the structure and
thickness of the citrate crown and rearrangement of citrate
molecules under the influence of NaCl. It was demonstrated
that taking into account the effects of polarization in the model
of a gold nanoparticle influenced the simulation results
concerning the distribution of citrate ions on the metal
surface. On the basis of electric potential visualization, the
mechanisms of interaction of polarizable gold nanoparticles
and citrate molecules were proposed.
We believe that it is possible to use this model as a starting
simulation point to investigate the interactions of citrate-
capped gold nanoparticles with other molecules, including
proteins and nucleic acids.
DOI: 10.1021/acs.jctc.8b00362
J. Chem. Theory Comput. 2019, 15, 1278−1292
Journal of Chemical Theory and Computation
■
*
ASSOCIATED CONTENT
S Supporting Information
The Supporting Information is available free of charge on the
ACS Publications website at DOI: 10.1021/acs.jctc.8b00362.
Preparing nanoparticle system for simulation; symmetric
equation for {111} and {100} planes; volumes above
Au(111) and Au(100) (Figure S1); final result of radial
distribution graphs (Figure S2); estimation of citrate
crown thickness; structure of citrate overlayers (Figures
S3−S10); normalized distribution of citrate mass centers
perpendicular to surfaces of the nanoparticle (Figures
S11−S18); citrate dynamics perpendicular to surface of
nanoparticle; density maps of water oxygen and
hydrogen atoms (Figure S19); visualization of electric
field potential (Figure S20); simulation results of
nonpolarizable gold nanoparticle model (Figure S21);
analysis of direct contacts of citrate molecules with
nonpolarizable nanoparticle model (Table S1); density
maps of different atoms in simulation of nanoparticle
(Figure S22); dynamics of system radial distribution
with NaCl (Figure S23) (PDF)
■
AUTHOR INFORMATION
Corresponding Authors
*Phone: +7 383-363-5134. Fax: +7 383-363-5134. E-mail:
pyshnyi@niboch.nsc.ru (D.V.P.).
*Phone: +7 383-363-5134. Fax: +7 383-363-5134. E-mail:
lomzov@niboch.nsc.ru (A.A.L.).
ORCID
Dmitrii V. Pyshnyi: 0000-0002-2587-3719
Alexander A. Lomzov: 0000-0003-3889-9464
Funding
This work was done in accordance with the State assignment
by the Russian State funded budget project (VI.62.1.4, 0309-
2016-0004), and the structural analysis of the interaction
between citrate ions and a gold nanoparticle (A.A.L.) was in
part supported by the Russian Science Foundation (grant No.
16-15-10156).
Notes
The authors declare no competing financial interest.
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1292 DOI: 10.1021/acs.jctc.8b00362

J. Chem. Theory Comput. 2019, 15, 1278−1292