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1 < \documentclass[journal = jctcce, manuscript = article]{achemso}
1 > \documentclass[journal = jpccck, manuscript = article]{achemso}
2   \setkeys{acs}{usetitle = true}
3  
4   \usepackage{caption}
# Line 17 | Line 17
17   \usepackage{graphicx}
18   \usepackage{achemso}
19   \usepackage{wrapfig}
20 < \usepackage[version=3]{mhchem}  % this is a great package for formatting chemical reactions
20 > \usepackage[version=3]{mhchem} % this is a great package for formatting chemical reactions
21   \usepackage{url}
22  
23 < \title{Simulations of Interfacial Thermal Conductance of Alkanethiolate Ligand-Protected Gold Nanoparticles}
23 > \title{The Thermal Conductance of Alkanethiolate-Protected Gold
24 >  Nanospheres: Effects of Curvature and Chain Length}
25  
26   \author{Kelsey M. Stocker}
27   \author{J. Daniel Gezelter}
28   \email{gezelter@nd.edu}
29 < \affiliation[University of Notre Dame]{251 Nieuwland Science Hall\\ Department of Chemistry and Biochemistry\\ University of Notre Dame\\ Notre Dame, Indiana 46556}
29 > \affiliation[University of Notre Dame]{251 Nieuwland Science Hall\\
30 > Department of Chemistry and Biochemistry\\
31 > University of Notre Dame\\
32 > Notre Dame, Indiana 46556}
33  
34 +
35 + \keywords{Nanoparticles, interfaces, thermal conductance}
36 +
37   \begin{document}
38  
39   \begin{tocentry}
40 < % \includegraphics[width=9cm]{figures/TOC}
40 > \center\includegraphics[width=3.9cm]{figures/TOC}
41   \end{tocentry}
42  
43   \newcolumntype{A}{p{1.5in}}
44   \newcolumntype{B}{p{0.75in}}
45  
39 % \author{Kelsey M. Stocker and J. Daniel
40 %   Gezelter\footnote{Corresponding author. \ Electronic mail:
41 %     gezelter@nd.edu} \\
42 %   251 Nieuwland Science Hall, \\
43 %       Department of Chemistry and Biochemistry,\\
44 %       University of Notre Dame\\
45 %       Notre Dame, Indiana 46556}
46  
47 %\date{\today}
48
49 %\maketitle
50
51 %\begin{doublespace}
52
47   \begin{abstract}
48          
49   \end{abstract}
# Line 61 | Line 55
55   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
56   \section{Introduction}
57  
58 + The thermal properties of various nanostructured interfaces have been
59 + the subject of intense experimental
60 + interest,\cite{Wilson:2002uq,PhysRevB.67.054302,doi:10.1021/jp048375k,PhysRevLett.96.186101,Wang10082007,doi:10.1021/jp8051888,PhysRevB.80.195406,doi:10.1021/la904855s}
61 + and the interfacial thermal conductance is the principal quantity of
62 + interest for understanding interfacial heat
63 + transport.\cite{cahill:793} Because nanoparticles have a significant
64 + fraction of their atoms at the particle / solvent interface, the
65 + chemical details of these interfaces govern the thermal transport
66 + properties.
67 +
68 + Previously, reverse non-equilibrium molecular dynamics (RNEMD) methods
69 + have been applied to calculate the interfacial thermal conductance at
70 + flat (111) metal / organic solvent interfaces that had been chemically
71 + protected by mixed-chain alkanethiolate groups.\cite{kuang:AuThl}
72 + These simulations suggested an explanation for the increase in thermal
73 + conductivity at alkanethiol-capped metal surfaces compared with bare
74 + metal interfaces.  Specifically, the chemical bond between the metal
75 + and the ligand introduces a vibrational overlap that is not present
76 + without the protecting group, and the overlap between the vibrational
77 + spectra (metal to ligand, ligand to solvent) provides a mechanism for
78 + rapid thermal transport across the interface. The simulations also
79 + suggested that this phenomenon is a non-monotonic function of the
80 + fractional coverage of the surface, as moderate coverages allow
81 + diffusive heat transport of solvent molecules that have been in close
82 + contact with the ligands.
83 +
84 + Simulations of {\it mixed-chain} alkylthiolate surfaces showed that
85 + solvent trapped close to the interface can be very efficient at moving
86 + thermal energy away from the surface.\cite{Stocker:2013cl} Trapped
87 + solvent molecules that were orientationally ordered with nearby
88 + ligands (but which were less able to diffuse into the bulk) were able
89 + to double the thermal conductance of the interface.  This indicates
90 + that the ligand-to-solvent vibrational energy transfer is the key
91 + feature for increasing particle-to-solvent thermal conductance.
92 +
93 + Recently, we extended RNEMD methods for use in non-periodic geometries
94 + by creating scaling/shearing moves between concentric regions of the
95 + simulation.\cite{Stocker:2014qq} In this work, we apply this
96 + non-periodic variant of RNEMD to investigate the role that {\it
97 +  curved} nanoparticle surfaces play in heat and mass transport.  On
98 + planar surfaces, we discovered that orientational ordering of surface
99 + protecting ligands had a large effect on the heat conduction from the
100 + metal to the solvent.  Smaller nanoparticles have high surface
101 + curvature that creates gaps in well-ordered self-assembled monolayers,
102 + and the effects those gaps have on the thermal conductance are unknown.
103 +
104 +
105 +
106   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
107   %               INTERFACIAL THERMAL CONDUCTANCE OF METALLIC NANOPARTICLES
108   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
109 < \section{Interfacial Thermal Conductance of Metallic Nanoparticles}
109 > %\section{Interfacial Thermal Conductance of Metallic Nanoparticles}
110  
111 < For a solvated nanoparticle, we can define a critical interfacial thermal conductance value,
111 > For a solvated nanoparticle, it is possible to define a critical value
112 > for the interfacial thermal conductance,
113   \begin{equation}
114 < G_c = \frac{3 C_f \Lambda_f}{r C_p}
114 > G_c = \frac{3 C_s \Lambda_s}{R C_p}
115   \end{equation}
116 + which depends on the solvent heat capacity, $C_s$, solvent thermal
117 + conductivity, $\Lambda_s$, particle radius, $R$, and nanoparticle heat
118 + capacity, $C_p$.\cite{Wilson:2002uq} In the limit of infinite
119 + interfacial thermal conductance, $G \gg G_c$, cooling of the
120 + nanoparticle is limited by the solvent properties, $C_s$ and
121 + $\Lambda_s$.  In the opposite limit, $G \ll G_c$, the heat dissipation
122 + is controlled by the thermal conductance of the particle / fluid
123 + interface. It is this regime with which we are concerned, where
124 + properties of ligands and the particle surface may be tuned to
125 + manipulate the rate of cooling for solvated nanoparticles.  Based on
126 + estimates of $G$ from previous simulations as well as experimental
127 + results for solvated nanostructures, gold nanoparticles solvated in
128 + hexane are in the $G \ll G_c$ regime for radii smaller than 40 nm. The
129 + particles included in this study are more than an order of magnitude
130 + smaller than this critical radius, so the heat dissipation should be
131 + controlled entirely by the surface features of the particle / ligand /
132 + solvent interface.
133  
74 dependent upon the fluid heat capacity, $C_f$, fluid thermal conductivity, $\Lambda_f$, particle radius, $r$, and nanoparticle heat capacity, $C_p$.\cite{Wilson:2002uq} In the infinite interfacial thermal conductance limit $G >> G_c$, the particle cooling rate is limited by the fluid properties, $C_f$ and $\Lambda_f$. In the opposite limit ($G << G_c$), the heat dissipation is controlled by the thermal conductance of the particle / fluid interface. It is this regime with which we are concerned, where properties of the interface may be tuned to manipulate the rate of cooling for a solvated nanoparticle. Based on $G$ values from previous simulations of gold nanoparticles solvated in hexane and experimental results for solvated nanostructures, it appears that we are in the $G << G_c$ regime for gold nanoparticles of radius $<$ 400 \AA\ solvated in hexane. The particles included in this study are more than an order of magnitude smaller than this critical radius. The heat dissipation should thus be controlled entirely by the surface features of the particle / ligand / solvent interface.
75
76 % Understanding how the structural details of the interfaces affect the energy flow between the particle and its surroundings is essential in designing and functionalizing metallic nanoparticles for use in plasmonic photothermal therapies,\cite{Jain:2007ux,Petrova:2007ad,Gnyawali:2008lp,Mazzaglia:2008to,Huff:2007ye,Larson:2007hw} which rely on the ability of metallic nanoparticles to absorb light in the near-IR, a portion of the spectrum in which living tissue is very nearly transparent. The relevant physical property controlling the transfer of this energy as heat into the surrounding tissue is the interfacial thermal conductance, $G$, which can be somewhat difficult to determine experimentally.\cite{Wilson:2002uq,Plech:2005kx}
77 %
78 % Metallic particles have also been proposed for use in efficient thermal-transfer fluids, although careful experiments by Eapen \textit{et al.} have shown that metal-particle-based nanofluids have thermal conductivities that match Maxwell predictions.\cite{Eapen:2007th} The likely cause of previously reported non-Maxwell behavior\cite{Eastman:2001wb,Keblinski:2002bx,Lee:1999ct,Xue:2003ya,Xue:2004oa} is percolation networks of nanoparticles exchanging energy via the solvent,\cite{Eapen:2007mw} so it is important to get a detailed molecular picture of particle-ligand and ligand-solvent interactions in order to understand the thermal behavior of complex fluids. To date, there have been some reported values from experiment\cite{Wilson:2002uq,doi:10.1021jp8051888,doi:10.1021jp048375k,Ge2005,Park2012}) of $G$ for ligand-protected nanoparticles embedded in liquids, but there is still a significant gap in knowledge about how chemically distinct ligands or protecting groups will affect heat transport from the particles. In particular, the dearth of atomistic, dynamic information available from molecular dynamics simulations means that the heat transfer mechanisms at these nanoparticle surfaces remain largely unclear.
79
134   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
135   %               STRUCTURE OF SELF-ASSEMBLED MONOLAYERS ON NANOPARTICLES
136   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
137 < \section{Structure of Self-Assembled Monolayers on Nanoparticles}
137 > \subsection{Structures of Self-Assembled Monolayers on Nanoparticles}
138  
139 < Though the ligand packing on planar surfaces is characterized for many different ligands and surface facets, it is not obvious \emph{a priori} how the same ligands will behave on the highly curved surfaces of nanoparticles. Thus, as more applications of ligand-stabilized nanostructures have become apparent, the structure and dynamics of ligands on metallic nanoparticles have been studied extensively.\cite{Badia1996:2,Badia1996,Henz2007,Badia1997:2,Badia1997,Badia2000} Badia, \textit{et al.} used transmission electron microscopy to determine that alkanethiol ligands on gold nanoparticles pack approximately 30\% more densely than on planar Au(111) surfaces.\cite{Badia1996:2} Subsequent experiments demonstrated that even at full coverages, surface curvature creates voids between linear ligand chains that can be filled via interdigitation of ligands on neighboring particles.\cite{Badia1996} The molecular dynamics simulations of Henz, \textit{et al.} indicate that at low coverages, the thiolate alkane chains will lie flat on the nanoparticle surface\cite{Henz2007} Above 90\% coverage, the ligands stand upright and recover the rigidity and tilt angle displayed on planar facets. Their simulations also indicate a high degree of mixing between the thiolate sulfur atoms and surface gold atoms at high coverages.
139 > Though the ligand packing on planar surfaces is characterized for many
140 > different ligands and surface facets, it is not obvious \emph{a
141 >  priori} how the same ligands will behave on the highly curved
142 > surfaces of spherical nanoparticles. Thus, as more applications of
143 > ligand-stabilized nanostructures have become apparent, the structure
144 > and dynamics of ligands on metallic nanoparticles have been studied
145 > extensively.\cite{Badia1996:2,Badia1996,Henz2007,Badia1997:2,Badia1997,Badia2000}
146 > Badia, \textit{et al.} used transmission electron microscopy to
147 > determine that alkanethiol ligands on gold nanoparticles pack
148 > approximately 30\% more densely than on planar Au(111)
149 > surfaces.\cite{Badia1996:2} Subsequent experiments demonstrated that
150 > even at full coverages, surface curvature creates voids between linear
151 > ligand chains that can be filled via interdigitation of ligands on
152 > neighboring particles.\cite{Badia1996} The molecular dynamics
153 > simulations of Henz, \textit{et al.} indicate that at low coverages,
154 > the thiolate alkane chains will lie flat on the nanoparticle
155 > surface\cite{Henz2007} Above 90\% coverage, the ligands stand upright
156 > and recover the rigidity and tilt angle displayed on planar
157 > facets. Their simulations also indicate a high degree of mixing
158 > between the thiolate sulfur atoms and surface gold atoms at high
159 > coverages.
160  
161 + To model thiolated gold nanospheres in this work, gold nanoparticles
162 + with radii ranging from 10 - 25 \AA\ were created from a bulk fcc
163 + lattice.  To match surface coverages previously reported by Badia,
164 + \textit{et al.}\cite{Badia1996:2}, these particles were passivated
165 + with a 50\% coverage of a selection of alkyl thiolates of varying
166 + chain lengths. The passivated particles were then solvated in hexane.
167 + Details of the models and simulation protocol follow in the next
168 + section.
169 +
170   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
171   %               NON-PERIODIC VSS-RNEMD METHODOLOGY
172   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
173 < \section{Non-Periodic Velocity Shearing and Scaling RNEMD Methodology}
173 > \subsection{Creating a thermal flux between particles and solvent}
174  
175 < Non-periodic VSS-RNEMD, explained in detail in Chapter 4, periodically applies a series of velocity scaling and shearing moves at regular intervals to impose a flux between two concentric spherical regions.
176 <
177 < To simultaneously impose a thermal flux ($J_r$) between the shells we
178 < use energy conservation constraints,
175 > The non-periodic variant of VSS-RNEMD\cite{Stocker:2014qq} applies a
176 > series of velocity scaling and shearing moves at regular intervals to
177 > impose a flux between two concentric spherical regions. To impose a
178 > thermal flux between the shells (without an accompanying angular
179 > shear), we solve for scaling coefficients $a$ and $b$,
180   \begin{eqnarray}
181 < K_a - J_r \Delta t & = & a^2 \left(K_a - \frac{1}{2}\langle
182 < \omega_a \rangle \cdot \overleftrightarrow{I_a} \cdot \langle \omega_a
99 < \rangle \right) + \frac{1}{2} \mathbf{c}_a \cdot \overleftrightarrow{I_a}
100 < \cdot \mathbf{c}_a \label{eq:Kc}\\
101 < K_b + J_r \Delta t & = & b^2 \left(K_b - \frac{1}{2}\langle
102 < \omega_b \rangle \cdot \overleftrightarrow{I_b} \cdot \langle \omega_b
103 < \rangle \right) + \frac{1}{2} \mathbf{c}_b \cdot \overleftrightarrow{I_b} \cdot \mathbf{c}_b \label{eq:Kh}
181 >        a = \sqrt{1 - \frac{q_r \Delta t}{K_a - K_a^\mathrm{rot}}}\\ \nonumber\\
182 >        b = \sqrt{1 + \frac{q_r \Delta t}{K_b - K_b^\mathrm{rot}}}
183   \end{eqnarray}
184 < Simultaneous solution of these quadratic formulae for the scaling coefficients, $a$ and $b$, will ensure that
185 < the simulation samples from the original microcanonical (NVE) ensemble. Here $K_{\{a,b\}}$ is the instantaneous
186 < translational kinetic energy of each shell. At each time interval, we solve for $a$, $b$, $\mathbf{c}_a$, and
187 < $\mathbf{c}_b$, subject to the imposed angular momentum flux, $j_r(\mathbf{L})$, and thermal flux, $J_r$,
188 < values.
184 > at each time interval.  These scaling coefficients conserve total
185 > kinetic energy and angular momentum subject to an imposed heat rate,
186 > $q_r$.  The coefficients also depend on the instantaneous kinetic
187 > energy, $K_{\{a,b\}}$, and the total rotational kinetic energy of each
188 > shell, $K_{\{a,b\}}^\mathrm{rot} = \sum_i m_i \left( \mathbf{v}_i
189 >  \times \mathbf{r}_i \right)^2 / 2$.
190  
191 + The scaling coefficients are determined and the velocity changes are
192 + applied at regular intervals,
193 + \begin{eqnarray}
194 +        \mathbf{v}_i \leftarrow a \left ( \mathbf{v}_i - \left < \omega_a \right > \times \mathbf{r}_i \right ) + \left < \omega_a \right > \times \mathbf{r}_i~~\:\\
195 +        \mathbf{v}_j \leftarrow b \left ( \mathbf{v}_j - \left < \omega_b \right > \times \mathbf{r}_j \right ) + \left < \omega_b \right > \times \mathbf{r}_j.
196 + \end{eqnarray}
197 + Here $\left < \omega_a \right > \times \mathbf{r}_i$ is the
198 + contribution to the velocity of particle $i$ due to the overall
199 + angular velocity of the $a$ shell. In the absence of an angular
200 + momentum flux, the angular velocity $\left < \omega_a \right >$ of the
201 + shell is nearly 0 and the resultant particle velocity is a nearly
202 + linear scaling of the initial velocity by the coefficient $a$ or $b$.
203 +
204 + Repeated application of this thermal energy exchange yields a radial
205 + temperature profile for the solvated nanoparticles that depends
206 + linearly on the applied heat rate, $q_r$. Similar to the behavior in
207 + the slab geometries, the temperature profiles have discontinuities at
208 + the interfaces between dissimilar materials.  The size of the
209 + discontinuity depends on the interfacial thermal conductance, which is
210 + the primary quantity of interest.
211 +
212   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
213   %               CALCULATING TRANSPORT PROPERTIES
214   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
114 \section{Calculating Transport Properties from Non-Periodic VSS-RNEMD}
115
215   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
216   %               INTERFACIAL THERMAL CONDUCTANCE
217   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
218   \subsection{Interfacial Thermal Conductance}
219  
220 < As described in Chapter 4, we can describe the thermal conductance of each spherical shell as the inverse Kapitza resistance. To describe the thermal conductance for an interface of considerable thickness, such as the ligand layers shown here, we can sum the individual thermal resistances of each concentric spherical shell to arrive at the total thermal resistance, or the inverse of the total interfacial thermal conductance:
220 > As described in earlier work,\cite{Stocker:2014qq} the thermal
221 > conductance of each spherical shell may be defined as the inverse
222 > Kapitza resistance of the shell. To describe the thermal conductance
223 > of an interface of considerable thickness -- such as the ligand layers
224 > shown here -- we can sum the individual thermal resistances of each
225 > concentric spherical shell to arrive at the inverse of the total
226 > interfacial thermal conductance. In slab geometries, the intermediate
227 > temperatures cancel, but for concentric spherical shells, the
228 > intermeidate temperatures and surface areas remain in the final sum,
229 > requiring the use of a series of individual resistance terms:
230  
231   \begin{equation}
232    \frac{1}{G} = R_\mathrm{total} = \frac{1}{q_r} \sum_i \left(T_{i+i} -
233      T_i\right) 4 \pi r_i^2.
234   \end{equation}
235  
236 < The longest ligand considered here is in excess of 15 \AA\ in length, requiring the use of at least 10 spherical shells to describe the total interfacial thermal conductance.
236 > The longest ligand considered here is in excess of 15 \AA\ in length,
237 > and we use 10 concentric spherical shells to describe the total
238 > interfacial thermal conductance of the ligand layer.
239  
240   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
241   %               COMPUTATIONAL DETAILS
# Line 137 | Line 247 | Gold -- gold interactions are described by the quantum
247   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
248   \subsection{Force Fields}
249  
250 < Gold -- gold interactions are described by the quantum Sutton-Chen (QSC) model,\cite{PhysRevB.59.3527} described in detail in Chapter 1.
250 > Throughout this work, gold -- gold interactions are described by the
251 > quantum Sutton-Chen (QSC) model.\cite{PhysRevB.59.3527} The hexane
252 > solvent is described by the TraPPE united atom
253 > model,\cite{TraPPE-UA.alkanes} where sites are located at the carbon
254 > centers for alkyl groups. The TraPPE-UA model for hexane provides both
255 > computational efficiency and reasonable accuracy for bulk thermal
256 > conductivity values. Bonding interactions were used for
257 > intra-molecular sites closer than 3 bonds. Effective Lennard-Jones
258 > potentials were used for non-bonded interactions.
259  
260 < Hexane molecules are described by the TraPPE united atom model,\cite{TraPPE-UA.alkanes} detailed in Chapter 3, which provides good computational efficiency and reasonable accuracy for bulk thermal conductivity values. In this model, sites are located at the carbon centers for alkyl groups. Bonding interactions, including bond stretches, bends and torsions, were used for intra-molecular sites closer than 3 bonds. For non-bonded interactions, Lennard-Jones potentials were used.
260 > To describe the interactions between metal (Au) and non-metal atoms,
261 > potential energy terms were adapted from an adsorption study of alkyl
262 > thiols on gold surfaces by Vlugt, \textit{et
263 >  al.}\cite{vlugt:cpc2007154} They fit an effective pair-wise
264 > Lennard-Jones form of potential parameters for the interaction between
265 > Au and pseudo-atoms CH$_x$ and S based on a well-established and
266 > widely-used effective potential of Hautman and Klein for the Au(111)
267 > surface.\cite{hautman:4994}
268  
144 To describe the interactions between metal (Au) and non-metal atoms, potential energy terms were adapted from an adsorption study of alkyl thiols on gold surfaces by Vlugt, \textit{et al.}\cite{vlugt:cpc2007154} They fit an effective pair-wise Lennard-Jones form of potential parameters for the interaction between Au and pseudo-atoms CH$_x$ and S based on a well-established and widely-used effective potential of Hautman and Klein for the Au(111) surface.\cite{hautman:4994}
269  
270 +
271   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
272   %               SIMULATION PROTOCOL
273   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
274   \subsection{Simulation Protocol}
275  
276 < The various sized gold nanoparticles were created from a bulk fcc lattice and were thermally equilibrated prior to the addition of ligands. A 50\% coverage of ligands (based on coverages reported by Badia, \textit{et al.}\cite{Badia1996:2}) were placed on the surface of the equilibrated nanoparticles using Packmol\cite{packmol}. The nanoparticle / ligand complexes were briefly thermally equilibrated before Packmol was used to solvate the structures within a spherical droplet of hexane. The thickness of the solvent layer was chosen to be at least 1.5$\times$ the radius of the nanoparticle / ligand structure. The fully solvated system was equilibrated in the Langevin Hull under 50 atm of pressure with a target temperature of 250 K for at least 1 nanosecond.
276 > Gold nanospheres with radii ranging from 10 - 25 \AA\ were created
277 > from a bulk fcc lattice and were thermally equilibrated prior to the
278 > addition of ligands. A 50\% coverage of ligands (based on coverages
279 > reported by Badia, \textit{et al.}\cite{Badia1996:2}) were placed on
280 > the surface of the equilibrated nanoparticles using
281 > Packmol\cite{packmol}. The nanoparticle / ligand complexes were
282 > thermally equilibrated before Packmol was used to solvate the
283 > structures inside a spherical droplet of hexane. The thickness of the
284 > solvent layer was chosen to be at least 1.5$\times$ the combined
285 > radius of the nanoparticle / ligand structure. The fully solvated
286 > system was equilibrated for at least 1 ns using the Langevin Hull to
287 > apply 50 atm of pressure and a target temperature of 250
288 > K.\cite{Vardeman2011} Typical system sizes ranged from 18,310 united
289 > atom sites for the 10 \AA particles with $C_4$ ligands to 89,490 sites
290 > for the 25 \AA particles with $C_{12}$ ligands.  Figure
291 > \ref{fig:NP25_C12h1} shows one of the solvated 25 \AA nanoparticles
292 > passivated with the $C_{12}$ ligands.  
293  
294 < Once equilibrated, thermal fluxes were applied for
295 < 1 nanosecond, until stable temperature gradients had
296 < developed. Systems were run under moderate pressure
297 < (50 atm) and average temperature (250K) to maintain a compact solvent cluster and avoid formation of a vapor phase near the heated metal surface.  Pressure was applied to the
298 < system via the non-periodic Langevin Hull.\cite{Vardeman2011} However,
299 < thermal coupling to the external temperature and pressure bath was
300 < removed to avoid interference with the imposed RNEMD flux.
294 > \begin{figure}
295 >        \includegraphics[width=\linewidth]{figures/NP25_C12h1}
296 >        \caption{A 25 \AA\ radius gold nanoparticle protected with a
297 >          half-monolayer of TraPPE-UA dodecanethiolate (C$_{12}$)
298 >          ligands and solvated in TraPPE-UA hexane. The interfacial
299 >          thermal conductance is computed by applying a kinetic energy
300 >          flux between the nanoparticle and an outer shell of
301 >          solvent.}
302 >        \label{fig:NP25_C12h1}
303 > \end{figure}
304  
305 < Because the method conserves \emph{total} angular momentum and energy, systems
306 < which contain a metal nanoparticle embedded in a significant volume of
307 < solvent will still experience nanoparticle diffusion inside the
308 < solvent droplet.  To aid in measuring an accurate temperature profile for these
309 < systems, a single gold atom at the origin of the coordinate system was
310 < assigned a mass $10,000 \times$ its original mass. The bonded and
311 < nonbonded interactions for this atom remain unchanged and the heavy
312 < atom is excluded from the RNEMD velocity scaling.  The only effect of this
169 < gold atom is to effectively pin the nanoparticle at the origin of the
170 < coordinate system, thereby preventing translational diffusion of the nanoparticle due to Brownian motion.
305 > Once equilibrated, thermal fluxes were applied for 1 ns, until stable
306 > temperature gradients had developed. Systems were run under moderate
307 > pressure (50 atm) with an average temperature (250K) that maintained a
308 > compact solvent cluster and avoided formation of a vapor layer near
309 > the heated metal surface.  Pressure was applied to the system via the
310 > non-periodic Langevin Hull.\cite{Vardeman2011} However, thermal
311 > coupling to the external temperature bath was removed to avoid
312 > interference with the imposed RNEMD flux.
313  
314 < %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
315 < %               INTERFACIAL THERMAL CONDUCTANCE
316 < %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
317 < \section{Interfacial Thermal Conductance}
314 > Because the method conserves \emph{total} angular momentum and energy,
315 > systems which contain a metal nanoparticle embedded in a significant
316 > volume of solvent will still experience nanoparticle diffusion inside
317 > the solvent droplet.  To aid in measuring an accurate temperature
318 > profile for these systems, a single gold atom at the origin of the
319 > coordinate system was assigned a mass $10,000 \times$ its original
320 > mass. The bonded and nonbonded interactions for this atom remain
321 > unchanged and the heavy atom is excluded from the RNEMD velocity
322 > scaling.  The only effect of this gold atom is to effectively pin the
323 > nanoparticle at the origin of the coordinate system, thereby
324 > preventing translational diffusion of the nanoparticle due to Brownian
325 > motion.
326  
327 + To provide statisical independence, five separate configurations were
328 + simulated for each particle radius and ligand length. The
329 + configurations were unique starting at the point of ligand placement
330 + in order to sample multiple surface-ligand configurations.
331 +
332 +
333   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
334   %               EFFECT OF PARTICLE SIZE
335   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
336 < \subsection{Effect of Particle Size}
336 > \section{Results}
337  
338 < I have modeled four sizes of nanoparticles ($r =$ 10, 15, 20, and 25 \AA). The smallest particle size produces the lowest interfacial thermal conductance value regardless of protecting group. Between the other three sizes of nanoparticles, there is no discernible dependence of the interfacial thermal conductance on the nanoparticle size. It is likely that the differences in local curvature of the nanoparticle sizes studied here do not disrupt the ligand packing and behavior in drastically different ways.
339 <
340 < \begin{figure}
341 <        \includegraphics[width=\linewidth]{figures/NPthiols_Gcombo}
342 <        \caption{Interfacial thermal conductance ($G$) and corrugation values for 4 sizes of solvated nanoparticles that are bare or protected with a 50\% coverage of C$_{4}$, C$_{8}$, or C$_{12}$ alkanethiolate ligands.}
343 <        \label{fig:NPthiols_Gcombo}
344 < \end{figure}
338 > We modeled four sizes of nanoparticles ($R =$ 10, 15, 20, and 25
339 > \AA). The smallest particle size produces the lowest interfacial
340 > thermal conductance values for most of the of protecting groups
341 > (Fig. \ref{fig:NPthiols_G}).  Between the other three sizes of
342 > nanoparticles, there is no discernible dependence of the interfacial
343 > thermal conductance on the nanoparticle size. It is likely that the
344 > differences in local curvature of the nanoparticle sizes studied here
345 > do not disrupt the ligand packing and behavior in drastically
346 > different ways.
347  
348   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
349   %               EFFECT OF LIGAND CHAIN LENGTH
350   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
193 \subsection{Effect of Ligand Chain Length}
351  
352 < I have studied three lengths of alkanethiolate ligands -- S(CH$_2$)$_3$CH$_3$, S(CH$_2$)$_7$CH$_3$, and S(CH$_2$)$_{11}$CH$_3$ -- referred to as C$_4$, C$_8$, and C$_{12}$ respectively, on each of the four nanoparticle sizes.
352 > We have also utilized half-monolayers of three lengths of
353 > alkanethiolate ligands -- S(CH$_2$)$_3$CH$_3$, S(CH$_2$)$_7$CH$_3$,
354 > and S(CH$_2$)$_{11}$CH$_3$ -- referred to as C$_4$, C$_8$, and
355 > C$_{12}$ respectively, in this study.
356  
357 < Unlike my previous study of varying thiolate ligand chain lengths on Au(111) surfaces, the interfacial thermal conductance of ligand-protected nanoparticles exhibits a distinct non-monotonic dependence on the ligand length. For the three largest particle sizes, a half-monolayer coverage of $C_4$ yields the highest interfacial thermal conductance and the next-longest ligand $C_8$ provides a nearly equivalent boost. The longest ligand $C_{12}$ offers only a marginal ($\sim$ 10 \%) increase in the interfacial thermal conductance over a bare nanoparticle.
357 > Unlike our previous study of varying thiolate ligand chain lengths on
358 > planar Au(111) surfaces, the interfacial thermal conductance of
359 > ligand-protected nanospheres exhibits a distinct dependence on the
360 > ligand length. For the three largest particle sizes, a half-monolayer
361 > coverage of $C_4$ yields the highest interfacial thermal conductance
362 > and the next-longest ligand, $C_8$, provides a similar boost. The
363 > longest ligand, $C_{12}$, offers only a nominal ($\sim$ 10 \%)
364 > increase in the interfacial thermal conductance over the bare
365 > nanoparticles.
366  
367 + \begin{figure}
368 +        \includegraphics[width=\linewidth]{figures/NPthiols_G}
369 +        \caption{Interfacial thermal conductance ($G$) values for 4
370 +          sizes of solvated nanoparticles that are bare or protected
371 +          with a 50\% coverage of C$_{4}$, C$_{8}$, or C$_{12}$
372 +          alkanethiolate ligands.}
373 +        \label{fig:NPthiols_G}
374 + \end{figure}
375 +
376   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
377   %               HEAT TRANSFER MECHANISMS
378   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
379 < \section{Mechanisms for Heat Transfer}
379 > \section{Mechanisms for Ligand-Enhanced Heat Transfer}
380  
204 \begin{figure}
205        \includegraphics[width=\linewidth]{figures/NPthiols_combo}
206        \caption{Computed solvent escape rates, ligand orientational P$_2$ values, and interfacial solvent orientational $P_2$ values for 4 sizes of solvated nanoparticles that are bare or protected with a 50\% coverage of C$_{4}$, C$_{8}$, or C$_{12}$ alkanethiolate ligands.}
207        \label{fig:NPthiols_combo}
208 \end{figure}
209
381   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
382   %               CORRUGATION OF PARTICLE SURFACE
383   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
384   \subsection{Corrugation of Particle Surface}
385  
386 < The bonding sites for thiols on gold surfaces have been studied extensively and include configurations beyond the traditional atop, bridge, and hollow sites found on planar surfaces. In particular, the deep potential well between the gold atoms and the thiolate sulfurs leads to insertion of the sulfur into the gold lattice and displacement of interfacial gold atoms. The degree of ligand-induced surface restructuring may have an impact on the interfacial thermal conductance and is an important phenomenon to quantify.
386 > The bonding sites for thiols on gold surfaces have been studied
387 > extensively and include configurations beyond the traditional atop,
388 > bridge, and hollow sites found on planar surfaces. In particular, the
389 > deep potential well between the gold atoms and the thiolate sulfurs
390 > leads to insertion of the sulfur into the gold lattice and
391 > displacement of interfacial gold atoms. The degree of ligand-induced
392 > surface restructuring may have an impact on the interfacial thermal
393 > conductance and is an important phenomenon to quantify.
394  
395 < Henz, \textit{et al.}\cite{Henz2007} used the metal density as a function of radius to measure the degree of mixing between the thiol sulfurs and surface gold atoms at the edge of a nanoparticle. Although metal density is important, disruption of the local crystalline ordering would have a large effect on the phonon spectrum in the particles. To measure this effect, I used the fraction of gold atoms exhibiting local fcc ordering as a function of radius to describe the ligand-induced disruption of the nanoparticle surface.
395 > Henz, \textit{et al.}\cite{Henz2007} used the metal density as a
396 > function of radius to measure the degree of mixing between the thiol
397 > sulfurs and surface gold atoms at the edge of a nanoparticle. Although
398 > metal density is important, disruption of the local crystalline
399 > ordering would also have a large effect on the phonon spectrum in the
400 > particles. To measure this effect, we use the fraction of gold atoms
401 > exhibiting local fcc ordering as a function of radius to describe the
402 > ligand-induced disruption of the nanoparticle surface.
403  
404 < The local bond orientational order can be described using the model proposed by Steinhardt \textit{et al.},\cite{Steinhardt1983} where spherical harmonics are associated with a central atom and its nearest neighbors. The local bonding environment, $\bar{q}_{\ell m}$, for each atom in the system can be determined by averaging over the spherical harmonics between the central atom and each of its neighbors. A global average orientational bond order parameter, $\bar{Q}_{\ell m}$, is the average over each $\bar{q}_{\ell m}$ for all atoms in the system. The third-order rotationally invariant combination of $\bar{Q}_{\ell m}$, $\hat{W}_4$, is utilized here. Ideal face-centered cubic (fcc), body-centered cubic (bcc), hexagonally close-packed (hcp), and simple cubic (sc), have values in the $\ell$ = 4 $\hat{W}$ invariant of -0.159, 0.134, 0.159, and 0.159, respectively. $\hat{W}_4$ has an extreme value for fcc structures, making it ideal for measuring local fcc order. The distribution of $\hat{W}_4$ local bond orientational order parameters, $p(\hat{W}_4)$, can provide information about individual atoms that are central to local fcc ordering.
404 > The local bond orientational order can be described using the method
405 > of Steinhardt \textit{et al.},\cite{Steinhardt1983} where spherical
406 > harmonics are associated with a central atom and its nearest
407 > neighbors. The local bonding environment, $\bar{q}_{\ell m}$, for each
408 > atom in the system can be determined by averaging over the spherical
409 > harmonics between the central atom and each of its neighbors,
410 > \begin{equation}
411 > \bar{q}_{\ell m} = \sum_i Y_\ell^m(\theta_i, \phi_i)
412 > \end{equation}
413 > where $\theta_i$ and $\phi_i$ are the relative angular coordinates of
414 > neighbor $i$ in the laboratory frame.  A global average orientational
415 > bond order parameter, $\bar{Q}_{\ell m}$, is the average over each
416 > $\bar{q}_{\ell m}$ for all atoms in the system. To remove the
417 > dependence on the laboratory coordinate frame, the third order
418 > rotationally invariant combination of $\bar{Q}_{\ell m}$,
419 > $\hat{w}_\ell$, is utilized here.\cite{Steinhardt1983,Vardeman:2008fk}
420  
421 < The fraction of fcc ordered gold atoms at a given radius
421 > For $\ell=4$, the ideal face-centered cubic (fcc), body-centered cubic
422 > (bcc), hexagonally close-packed (hcp), and simple cubic (sc) local
423 > structures exhibit $\hat{w}_4$ values of -0.159, 0.134, 0.159, and
424 > 0.159, respectively. Because $\hat{w}_4$ exhibits an extreme value for
425 > fcc structures, this makes it ideal for measuring local fcc
426 > ordering. The spatial distribution of $\hat{w}_4$ local bond
427 > orientational order parameters, $p(\hat{w}_4 , r)$, can provide
428 > information about the location of individual atoms that are central to
429 > local fcc ordering.
430  
431 + The fraction of fcc-ordered gold atoms at a given radius in the
432 + nanoparticle,
433   \begin{equation}
434 <        f_{fcc} = \int_{-\infty}^{w_i} p(\hat{W}_4) d \hat{W}_4
434 >        f_\mathrm{fcc}(r) = \int_{-\infty}^{w_c} p(\hat{w}_4, r) d \hat{w}_4
435   \end{equation}
436 + is described by the distribution of the local bond orientational order
437 + parameters, $p(\hat{w}_4, r)$, and $w_c$, a cutoff for the peak
438 + $\hat{w}_4$ value displayed by fcc structures. A $w_c$ value of -0.12
439 + was chosen to isolate the fcc peak in $\hat{w}_4$.
440  
441 < is described by the distribution of the local bond orientational order parameter, $p(\hat{W}_4)$, and $w_i$, a cutoff for the peak $\hat{W}_4$ value displayed by fcc structures. A $w_i$ value of -0.12 was chosen to isolate the fcc peak in $\hat{W}_4$.
441 > As illustrated in Figure \ref{fig:Corrugation}, the presence of
442 > ligands decreases the fcc ordering of the gold atoms at the
443 > nanoparticle surface. For the smaller nanoparticles, this disruption
444 > extends into the core of the nanoparticle, indicating widespread
445 > disruption of the lattice.
446  
229 As illustrated in Figure \ref{fig:Corrugation}, the presence of ligands decreases the fcc ordering of the gold atoms at the nanoparticle surface. For the smaller nanoparticles, this disruption extends into the core of the nanoparticle, indicating widespread disruption of the lattice.
230
447   \begin{figure}
448          \includegraphics[width=\linewidth]{figures/NP10_fcc}
449 <        \caption{Fraction of gold atoms with fcc ordering as a function of radius for a 10 \AA\ radius nanoparticle. The decreased fraction of fcc ordered atoms in ligand-protected nanoparticles relative to bare particles indicates restructuring of the nanoparticle surface by the thiolate sulfur atoms.}
449 >        \caption{Fraction of gold atoms with fcc ordering as a
450 >          function of radius for a 10 \AA\ radius nanoparticle. The
451 >          decreased fraction of fcc-ordered atoms in ligand-protected
452 >          nanoparticles relative to bare particles indicates
453 >          restructuring of the nanoparticle surface by the thiolate
454 >          sulfur atoms.}
455          \label{fig:Corrugation}
456   \end{figure}
457  
458 < We may describe the thickness of the disrupted nanoparticle surface by defining a corrugation factor, $c$, as the ratio of the radius at which the fraction of gold atoms with fcc ordering is 0.9 and the radius at which the fraction is 0.5.
458 > We may describe the thickness of the disrupted nanoparticle surface by
459 > defining a corrugation factor, $c$, as the ratio of the radius at
460 > which the fraction of gold atoms with fcc ordering is 0.9 and the
461 > radius at which the fraction is 0.5.
462  
463   \begin{equation}
464 <        c = 1 - \frac{r(f_{fcc} = 0.9)}{r(f_{fcc} = 0.5)}
464 >        c = 1 - \frac{r(f_\mathrm{fcc} = 0.9)}{r(f_\mathrm{fcc} = 0.5)}
465   \end{equation}
466  
467 < A clean, unstructured interface will have a sharp drop in $f_{fcc}$ at the edge of the particle ($c \rightarrow$ 0). In the opposite limit where the entire nanoparticle surface is restructured, the radius at which there is a high probability of fcc ordering moves dramatically inward ($c \rightarrow$ 1).
467 > A sharp interface will have a sharp drop in $f_\mathrm{fcc}$ at the
468 > edge of the particle ($c \rightarrow$ 0). In the opposite limit where
469 > the entire nanoparticle surface is restructured by ligands, the radius
470 > at which there is a high probability of fcc ordering moves
471 > dramatically inward ($c \rightarrow$ 1).
472  
473 < The computed corrugation factors are shown in Figure \ref{fig:NPthiols_Gcombo} for bare nanoparticles and for ligand-protected particles as a function of ligand chain length. The largest nanoparticles are only slightly restructured by the presence of ligands on the surface, while the smallest particle ($r$ = 10 \AA) exhibits significant disruption of the original fcc ordering when covered with a half-monolayer of thiol ligands.
473 > The computed corrugation factors are shown in Figure
474 > \ref{fig:NPthiols_combo} for bare nanoparticles and for
475 > ligand-protected particles as a function of ligand chain length. The
476 > largest nanoparticles are only slightly restructured by the presence
477 > of ligands on the surface, while the smallest particle ($r$ = 10 \AA)
478 > exhibits significant disruption of the original fcc ordering when
479 > covered with a half-monolayer of thiol ligands.
480  
481 + Because the thiolate ligands do not significantly alter the larger
482 + particle crystallinity, the surface corrugation does not seem to be a
483 + likely candidate to explain the large increase in thermal conductance
484 + at the interface.
485 +
486   % \begin{equation}
487   %       C = \frac{r_{bare}(\rho_{\scriptscriptstyle{0.85}}) - r_{capped}(\rho_{\scriptscriptstyle{0.85}})}{r_{bare}(\rho_{\scriptscriptstyle{0.85}})}.
488   % \end{equation}
489   %
490   % Here, $r_{bare}(\rho_{\scriptscriptstyle{0.85}})$ is the radius of a bare nanoparticle at which the density is $85\%$ the bulk value and $r_{capped}(\rho_{\scriptscriptstyle{0.85}})$ is the corresponding radius for a particle of the same size with a layer of ligands. $C$ has a value of 0 for a bare particle and approaches $1$ as the degree of surface atom mixing increases.
491  
492 +
493 +
494 + \begin{figure}
495 +        \includegraphics[width=\linewidth]{figures/NPthiols_combo}
496 +        \caption{Computed corrugation values, solvent escape rates,
497 +          ligand orientational $P_2$ values, and interfacial solvent
498 +          orientational $P_2$ values for 4 sizes of solvated
499 +          nanoparticles that are bare or protected with a 50\%
500 +          coverage of C$_{4}$, C$_{8}$, or C$_{12}$ alkanethiolate
501 +          ligands.}
502 +        \label{fig:NPthiols_combo}
503 + \end{figure}
504 +
505 +
506   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
507   %               MOBILITY OF INTERFACIAL SOLVENT
508   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
509   \subsection{Mobility of Interfacial Solvent}
510  
511 < As in the planar case described in Chapter 3, I use a survival correlation function, $C(t)$, to measure the residence time of a solvent molecule in the nanoparticle thiolate layer. This function correlates the identity of all hexane molecules within the radial range of the thiolate layer at two separate times. If the solvent molecule is present at both times, the configuration contributes a $1$, while the absence of the molecule at the later time indicates that the solvent molecule has migrated into the bulk, and this configuration contributes a $0$. A steep decay in $C(t)$ indicates a high turnover rate of solvent molecules from the chain region to the bulk. We may define the escape rate for trapped solvent molecules at the interface as
512 <
511 > Another possible mechanism for increasing interfacial conductance is
512 > the mobility of the interfacial solvent.  We used a survival
513 > correlation function, $C(t)$, to measure the residence time of a
514 > solvent molecule in the nanoparticle thiolate
515 > layer.\cite{Stocker:2013cl} This function correlates the identity of
516 > all hexane molecules within the radial range of the thiolate layer at
517 > two separate times. If the solvent molecule is present at both times,
518 > the configuration contributes a $1$, while the absence of the molecule
519 > at the later time indicates that the solvent molecule has migrated
520 > into the bulk, and this configuration contributes a $0$. A steep decay
521 > in $C(t)$ indicates a high turnover rate of solvent molecules from the
522 > chain region to the bulk. We may define the escape rate for trapped
523 > solvent molecules at the interface as
524   \begin{equation}
525 < k_{escape} = \left( \int_0^T C(t) dt \right)^{-1}
525 > k_\mathrm{escape} = \left( \int_0^T C(t) dt \right)^{-1}
526    \label{eq:mobility}
527   \end{equation}
528 + where T is the length of the simulation. This is a direct measure of
529 + the rate at which solvent molecules initially entangled in the
530 + thiolate layer can escape into the bulk. When $k_\mathrm{escape}
531 + \rightarrow 0$, the solvent becomes permanently trapped in the
532 + interfacial region.
533  
534 < where T is the length of the simulation. This is a direct measure of the rate at which solvent molecules initially entangled in the thiolate layer can escape into the bulk. As $k_{escape} \rightarrow 0$, the solvent becomes permanently trapped in the interfacial region.
534 > The solvent escape rates for bare and ligand-protected nanoparticles
535 > are shown in Figure \ref{fig:NPthiols_combo}. As the ligand chain
536 > becomes longer and more flexible, interfacial solvent molecules become
537 > trapped in the ligand layer and the solvent escape rate decreases.
538 > This mechanism contributes a partial explanation as to why the longer
539 > ligands have significantly lower thermal conductance.
540  
267 The solvent escape rates for bare and ligand-protected nanoparticles are shown in Figure \ref{fig:NPthiols_combo}. As the ligand chain becomes longer and more flexible, interfacial solvent molecules becomes trapped in the ligand layer and the solvent escape rate decreases.
268
541   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
542   %               ORIENTATION OF LIGAND CHAINS
543   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
544   \subsection{Orientation of Ligand Chains}
545  
546 < I have previously observed that as the ligand chain length increases in length, it becomes significantly more flexible. Thus, different lengths of ligands should favor different chain orientations on the surface of the nanoparticle. To determine the distribution of ligand orientations relative to the particle surface I examine the probability of each $\cos{(\theta)}$,
547 <
546 > As the ligand chain length increases in length, it exhibits
547 > significantly more conformational flexibility. Thus, different lengths
548 > of ligands should favor different chain orientations on the surface of
549 > the nanoparticle. To determine the distribution of ligand orientations
550 > relative to the particle surface we examine the probability of
551 > finding a ligand with a particular orientation relative to the surface
552 > normal of the nanoparticle,
553   \begin{equation}
554   \cos{(\theta)}=\frac{\vec{r}_i\cdot\hat{u}_i}{|\vec{r}_i||\hat{u}_i|}
555   \end{equation}
556 + where $\vec{r}_{i}$ is the vector between the cluster center of mass
557 + and the sulfur atom on ligand molecule {\it i}, and $\hat{u}_{i}$ is
558 + the vector between the sulfur atom and \ce{CH3} pseudo-atom on ligand
559 + molecule {\it i}. As depicted in Figure \ref{fig:NP_pAngle}, $\theta
560 + \rightarrow 180^{\circ}$ for a ligand chain standing upright on the
561 + particle ($\cos{(\theta)} \rightarrow -1$) and $\theta \rightarrow
562 + 90^{\circ}$ for a ligand chain lying down on the surface
563 + ($\cos{(\theta)} \rightarrow 0$). As the thiolate alkane chain
564 + increases in length and becomes more flexible, the ligands are more
565 + willing to lie down on the nanoparticle surface and exhibit increased
566 + population at $\cos{(\theta)} = 0$.
567  
280 where $\vec{r}_{i}$ is the vector between the cluster center of mass and the sulfur atom on ligand molecule {\it i}, and $\hat{u}_{i}$ is the vector between the sulfur atom and CH3 pseudo-atom on ligand molecule {\it i}. As depicted in Figure \ref{fig:NP_pAngle}, $\theta \rightarrow 180^{\circ}$ for a ligand chain standing upright on the particle ($\cos{(\theta)} \rightarrow -1$) and $\theta \rightarrow 90^{\circ}$ for a ligand chain lying down on the surface ($\cos{(\theta)} \rightarrow 0$). As the thiolate alkane chain increases in length and becomes more flexible, the ligands are more likely to lie down on the nanoparticle surface and there will be increased population at $\cos{(\theta)} = 0$.
281
568   \begin{figure}
569          \includegraphics[width=\linewidth]{figures/NP_pAngle}
570 <        \caption{The two extreme cases of ligand orientation relative to the nanoparticle surface: the ligand completely outstretched ($\cos{(\theta)} = -1$) and the ligand fully lying down on the particle surface ($\cos{(\theta)} = 0$).}
570 >        \caption{The two extreme cases of ligand orientation relative
571 >          to the nanoparticle surface: the ligand completely
572 >          outstretched ($\cos{(\theta)} = -1$) and the ligand fully
573 >          lying down on the particle surface ($\cos{(\theta)} = 0$).}
574          \label{fig:NP_pAngle}
575   \end{figure}
576  
# Line 291 | Line 580 | A single number describing the average ligand chain or
580   %       \label{fig:thiol_pAngle}
581   % \end{figure}
582  
583 < A single number describing the average ligand chain orientation relative to the nanoparticle surface may be achieved by calculating a P$_2$ order parameter from the distribution of $\cos(\theta)$ values.
584 <
583 > An order parameter the average ligand chain orientation relative to
584 > the nanoparticle surface is available using the second order Legendre
585 > parameter,
586   \begin{equation}
587 <        P_2(\cos(\theta)) = \left < \frac{1}{2} \left (3\cos^2(\theta) - 1 \right ) \right >
587 >        P_2 = \left< \frac{1}{2} \left(3\cos^2(\theta) - 1 \right) \right>
588   \end{equation}
589  
590 < A ligand chain that is perpendicular to the particle surface has a P$_2$ value of 1, while a ligand chain lying flat on the nanoparticle surface has a P$_2$ value of $-\frac{1}{2}$. Disordered ligand layers will exhibit a mean P$_2$ value of 0. As shown in Figure \ref{fig:NPthiols_combo} the ligand P$_2$ value approaches 0 as ligand chain length -- and ligand flexibility -- increases.
590 > Ligand populations that are perpendicular to the particle surface hav
591 > P$_2$ values of 1, while ligand populations lying flat on the
592 > nanoparticle surface have P$_2$ values of $-0.5$. Disordered ligand
593 > layers will exhibit mean P$_2$ values of 0. As shown in Figure
594 > \ref{fig:NPthiols_combo} the ligand P$_2$ values approaches 0 as
595 > ligand chain length -- and ligand flexibility -- increases.
596  
597   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
598   %               ORIENTATION OF INTERFACIAL SOLVENT
599   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
600   \subsection{Orientation of Interfacial Solvent}
601  
602 < I also examined the distribution of \emph{hexane} molecule orientations relative to the particle surface using the same $\cos{(\theta)}$ analysis utilized for the ligand chain orientations. In this case, $\vec{r}_i$ is the vector between the particle center of mass and one of the \ce{CH2} pseudo-atoms in the middle of hexane molecule $i$ and $\hat{u}_i$ is the vector between the two \ce{CH3} pseudo-atoms on molecule $i$. Since we are only interested in the orientation of solvent molecules near the ligand layer, I selected only the hexane molecules within a specific $r$-range, between the edge of the particle and the end of the ligand chains. A large population of hexane molecules with $\cos{(\theta)} \cong -1$ would indicate interdigitation of the solvent molecules between the upright ligand chains. A more random distribution of $\cos{(\theta)}$ values indicates either little penetration of the ligand layer by the solvent, or a very disordered arrangement of ligand chains on the particle surface. Again, P$_2$ order parameter values may be obtained from the distribution of $\cos(\theta)$ values.
602 > Similarly, we examined the distribution of \emph{hexane} molecule
603 > orientations relative to the particle surface using the same angular
604 > analysis utilized for the ligand chain orientations. In this case,
605 > $\vec{r}_i$ is the vector between the particle center of mass and one
606 > of the \ce{CH2} pseudo-atoms in the middle of hexane molecule $i$ and
607 > $\hat{u}_i$ is the vector between the two \ce{CH3} pseudo-atoms on
608 > molecule $i$. Since we are only interested in the orientation of
609 > solvent molecules near the ligand layer, we select only the hexane
610 > molecules within a specific $r$-range, between the edge of the
611 > particle and the end of the ligand chains. A large population of
612 > hexane molecules with $\cos{(\theta)} \cong \pm 1$ would indicate
613 > interdigitation of the solvent molecules between the upright ligand
614 > chains. A more random distribution of $\cos{(\theta)}$ values
615 > indicates a disordered arrangement of solvent chains on the particle
616 > surface. Again, P$_2$ order parameter values provide a population
617 > analysis for the solvent that is close to the particle surface.
618  
619 < The average orientation of the interfacial solvent molecules is notably flat on the \emph{bare} nanoparticle surface. This blanket of hexane molecules on the particle surface may act as an insulating layer, increasing the interfacial thermal resistance. As the length (and flexibility) of the ligand increases, the average interfacial solvent P$_2$ value approaches 0, indicating random orientation of the ligand chains. The average orientation of solvent within the $C_8$ and $C_{12}$ ligand layers is essentially totally random. Solvent molecules in the interfacial region of $C_4$ ligand-protected nanoparticles do not lie as flat on the surface as in the case of the bare particles, but are not as random as the longer ligand lengths.
619 > The average orientation of the interfacial solvent molecules is
620 > notably flat on the \emph{bare} nanoparticle surfaces. This blanket of
621 > hexane molecules on the particle surface may act as an insulating
622 > layer, increasing the interfacial thermal resistance. As the length
623 > (and flexibility) of the ligand increases, the average interfacial
624 > solvent P$_2$ value approaches 0, indicating a more random orientation
625 > of the ligand chains. The average orientation of solvent within the
626 > $C_8$ and $C_{12}$ ligand layers is essentially random. Solvent
627 > molecules in the interfacial region of $C_4$ ligand-protected
628 > nanoparticles do not lie as flat on the surface as in the case of the
629 > bare particles, but are not as randomly oriented as the longer ligand
630 > lengths.
631  
632 < These results are particularly interesting in light of the results described in Chapter 3, where solvent molecules readily filled the vertical gaps between neighboring ligand chains and there was a strong correlation between ligand and solvent molecular orientations. It appears that the introduction of surface curvature and a lower ligand packing density creates a very disordered ligand layer that lacks well-formed channels for the solvent molecules to occupy.
632 > These results are particularly interesting in light of our previous
633 > results\cite{Stocker:2013cl}, where solvent molecules readily filled
634 > the vertical gaps between neighboring ligand chains and there was a
635 > strong correlation between ligand and solvent molecular
636 > orientations. It appears that the introduction of surface curvature
637 > and a lower ligand packing density creates a disordered ligand layer
638 > that lacks well-formed channels for the solvent molecules to occupy.
639  
640   % \begin{figure}
641   %       \includegraphics[width=\linewidth]{figures/hex_pAngle}
# Line 321 | Line 648 | We may also determine the extent of ligand -- solvent
648   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
649   \subsection{Solvent Penetration of Ligand Layer}
650  
651 < We may also determine the extent of ligand -- solvent interaction by calculating the hexane density as a function of $r$. Figure \ref{fig:hex_density} shows representative radial hexane density profiles for a solvated 25 \AA\ radius nanoparticle with no ligands, and 50\% coverage of C$_{4}$, C$_{8}$, and C$_{12}$ thiolates.
651 > We may also determine the extent of ligand -- solvent interaction by
652 > calculating the hexane density as a function of radius. Figure
653 > \ref{fig:hex_density} shows representative radial hexane density
654 > profiles for a solvated 25 \AA\ radius nanoparticle with no ligands,
655 > and 50\% coverage of C$_{4}$, C$_{8}$, and C$_{12}$ thiolates.
656  
657   \begin{figure}
658          \includegraphics[width=\linewidth]{figures/hex_density}
659 <        \caption{Radial hexane density profiles for 25 \AA\ radius nanoparticles with no ligands (circles), C$_{4}$ ligands (squares), C$_{8}$ ligands (triangles), and C$_{12}$ ligands (diamonds). As ligand chain length increases, the nearby solvent is excluded from the ligand layer. Some solvent is present inside the particle $r_{max}$ location due to faceting of the nanoparticle surface.}
659 >        \caption{Radial hexane density profiles for 25 \AA\ radius
660 >          nanoparticles with no ligands (circles), C$_{4}$ ligands
661 >          (squares), C$_{8}$ ligands (triangles), and C$_{12}$ ligands
662 >          (diamonds). As ligand chain length increases, the nearby
663 >          solvent is excluded from the ligand layer. Some solvent is
664 >          present inside the particle $r_{max}$ location due to
665 >          faceting of the nanoparticle surface.}
666          \label{fig:hex_density}
667   \end{figure}
668  
669 < The differences between the radii at which the hexane surrounding the ligand-covered particles reaches bulk density correspond nearly exactly to the differences between the lengths of the ligand chains. Beyond the edge of the ligand layer, the solvent reaches its bulk density within a few angstroms. The differing shapes of the density curves indicate that the solvent is increasingly excluded from the ligand layer as the chain length increases.
669 > The differences between the radii at which the hexane surrounding the
670 > ligand-covered particles reaches bulk density correspond nearly
671 > exactly to the differences between the lengths of the ligand
672 > chains. Beyond the edge of the ligand layer, the solvent reaches its
673 > bulk density within a few angstroms. The differing shapes of the
674 > density curves indicate that the solvent is increasingly excluded from
675 > the ligand layer as the chain length increases.
676  
677   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
678   %               DISCUSSION
679   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
680   \section{Discussion}
681  
682 < The chemical bond between the metal and the ligand introduces vibrational overlap that is not present between the bare metal surface and solvent. Thus, regardless of ligand chain length, the presence of a half-monolayer ligand coverage yields a higher interfacial thermal conductance value than the bare nanoparticle. The dependence of the interfacial thermal conductance on ligand chain length is primarily explained by increased ligand flexibility. The shortest and least flexible ligand ($C_4$), which exhibits the highest interfacial thermal conductance value, is oriented more normal to the particle surface than the longer ligands and is least likely to trap solvent molecules within the ligand layer. The longer $C_8$ and $C_{12}$ ligands have increasingly disordered average orientations and correspondingly lower solvent escape rates.
682 > The chemical bond between the metal and the ligand introduces
683 > vibrational overlap that is not present between the bare metal surface
684 > and solvent. Thus, regardless of ligand chain length, the presence of
685 > a half-monolayer ligand coverage yields a higher interfacial thermal
686 > conductance value than the bare nanoparticle. The dependence of the
687 > interfacial thermal conductance on ligand chain length is primarily
688 > explained by increased ligand flexibility and a corresponding decrease
689 > in solvent mobility away from the particles.  The shortest and least
690 > flexible ligand ($C_4$), which exhibits the highest interfacial
691 > thermal conductance value, has a smaller range of angles relative to
692 > the surface normal and is least likely to trap solvent molecules
693 > within the ligand layer. The longer $C_8$ and $C_{12}$ ligands have
694 > increasingly disordered orientations and correspondingly lower solvent
695 > escape rates.
696  
697 < The heat transfer mechanisms proposed in Chapter 3 can also be applied to the non-periodic case. When the ligands are less tightly packed, the cooperative orientational ordering between the ligand and solvent decreases dramatically and the conductive heat transfer model plays a much smaller role in determining the total interfacial thermal conductance. Thus, heat transfer into the solvent relies primarily on the convective model, where solvent molecules pick up thermal energy from the ligands and diffuse into the bulk solvent. This mode of heat transfer is hampered by a slow solvent escape rate, which is clearly present in the randomly ordered long ligand layers.
697 > When the ligands are less tightly packed, the cooperative
698 > orientational ordering between the ligand and solvent decreases
699 > dramatically and the conductive heat transfer model plays a much
700 > smaller role in determining the total interfacial thermal
701 > conductance. Thus, heat transfer into the solvent relies primarily on
702 > the convective model, where solvent molecules pick up thermal energy
703 > from the ligands and diffuse into the bulk solvent. This mode of heat
704 > transfer is hampered by a slow solvent escape rate, which is clearly
705 > present in the randomly ordered long ligand layers.
706  
707   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
708   % **ACKNOWLEDGMENTS**
709   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
710   \begin{acknowledgement}
711    Support for this project was provided by the National Science Foundation
712 <  under grant CHE-0848243. Computational time was provided by the
712 >  under grant CHE-1362211. Computational time was provided by the
713    Center for Research Computing (CRC) at the University of Notre Dame.
714   \end{acknowledgement}
715  
# Line 354 | Line 718 | The heat transfer mechanisms proposed in Chapter 3 can
718  
719   \bibliography{NPthiols}
720  
721 < \end{document}
721 > \end{document}

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