Gold-Carbon Contacts from Oxidative Addition of Aryl Iodides

Article abstract of DOI:10.1021/jacs.0c01466

Aryl halides are ubiquitous functional groups in organic chemistry, yet despite their obvious appeal as surface-binding linkers and as precursors for controlled graphene nanoribbon synthesis, they have seldom been used as such in molecular electronics. The confusion regarding the bonding of aryl iodides to Au electrodes is a case in point, with ambiguous reports of both dative Au-I and covalent Au-C contacts. Here we form single-molecule junctions with a series of oligophenylene molecular wires terminated asymmetrically with iodine and thiomethyl to show that the dative Au-I contact has a lower conductance than the covalent Au-C interaction, which we propose occurs via an in situ oxidative addition reaction at the Au surface. Furthermore, we confirm the formation of the Au-C bond by measuring an analogous series of molecules prepared ex situ with the complex Au^I(PPh₃) in place of the iodide. Density functional theory-based transport calculations support our experimental observations that Au-C linkages have higher conductance than Au-I linkages. Finally, we demonstrate selective promotion of the Au-C bond formation by controlling the bias applied across the junction. In addition to establishing the different binding modes of aryl iodides, our results chart a path to actively controlling oxidative addition on an Au surface using an applied bias.

Full text of DOI:10.1021/jacs.0c01466

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Article
Gold-Carbon Contacts from Oxidative Addition of Aryl Iodides
Rachel L. Starr, Tianren Fu, Evan A. Doud, Ilana Stone, Xavier Roy, and Latha Venkataraman
J. Am. Chem. Soc., Just Accepted Manuscript • DOI: 10.1021/jacs.0c01466 • Publication Date (Web): 26 Mar 2020
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Gold-Carbon Contacts from Oxidative Addition of Aryl Iodides
Rachel L. Starr,† Tianren Fu,† Evan A. Doud,† Ilana Stone,† Xavier Roy,*,† Latha Venkataraman*,†,‡
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†Department of Chemistry, ‡Department of Applied Physics and Mathematics, Columbia University, New York, New York
10027, United States
ABSTRACT: Aryl halide are ubiquitous functional groups in organic chemistry, yet despite their obvious appeal as surface-binding
linkers and as precursors for controlled graphene nanoribbon synthesis, they have seldom been used as such in molecular electronics.
The confusion regarding the bonding of aryl iodides to Au electrodes is a case in point, with ambiguous reports of both dative AuI
and covalent AuC contacts. Here we form single-molecule junctions with a series of oligophenylene molecular wires terminated
asymmetrically with iodine and thiomethyl to show that the dative Au–I contact has a lower conductance than the covalent Au–C
interaction, which we propose occurs via an in situ oxidative addition reaction at the Au surface. Furthermore, we confirm the
formation of the Au–C bond by measuring an analogous series of molecules prepared ex situ with the complex AuI(PPh3) in place of
the iodide. Density functional theory-based transport calculations support our experimental observations that Au–C linkages have
higher conductance than Au–I linkages. Finally, we demonstrate selective promotion of the Au–C bond formation by controlling the
bias applied across the junction. In addition to establishing the different binding modes of aryl iodides, our results chart a path to
actively controlling oxidative addition on an Au surface using an applied bias.
INTRODUCTION
In this work, we measure the single-molecule conductance of
a series of asymmetric oligophenylene molecules with an iodide
on one end and a thiomethyl group on the other. We
demonstrate that the aryl iodide moiety undergoes a voltage-
induced oxidative addition reaction on the Au surface to form a
single molecule junction connected through a covalent AuC
bond. The formation of the AuC bond is validated by
measuring the conductance of the molecules in situ and
comparing these values to control compounds prepared ex situ
with the complex AuI(PPh3) in place of the iodide. Our
experimental measurements and supporting transport
calculations based on density functional theory (DFT) reveal
that junctions formed via AuC bonds display an increased
conductance when compared to junctions formed through a
dative AuI interaction. Moreover, we show that the proposed
surface-based oxidative addition mechanism can be modulated
by applying a voltage, wherein one electrode is polarized to
increase its chemical potential, selectively promoting the
reaction.
The controlled binding of single molecules between
nanoscopic metal electrodes is a critical step in the design and
assembly of molecular electronic devices. The specific binding
groups, or linkers, on the molecule establish the mechanical
connections to the electrodes and couple the discrete molecular
orbitals to the electronic bands of the electrodes. Studying
charge transport across the resulting metal-organic interfaces
provides fundamental understanding of the nature of these
contacts. Typical linkers used to bind organic molecules to
metal electrodes include thiols,1,2 thioethers,3 and amines.4
Although aryl halides are an extremely common and
synthetically accessible functional group in organic chemistry,
they have been used infrequently as linkers in molecular
electronic applications. As a result, the binding motifs and
electronic coupling strength of aryl halides are poorly
understood. For example, some prior work with aryl iodides
have reported dative AuI contacts,5,6 while others have
suggested without substantial evidence that the iodide
dissociates from the molecule, yielding a direct AuC bond.7
Such linkages are particularly attractive for single molecule
electronics, as covalent interactions generally lead to an
increase in conductance.8 Junctions with AuC linkages have
been achieved using alkyne linkers9,10,11 and trimethyl tin-
functionalized precursors,8,12,13 however these methods
typically involve intensive syntheses, toxic chemicals, and are
typically limited to select organic backbones. Aryl halides have
also been used as precursors for the synthesis of graphene
nanoribbons, an important component of next generation
nanoscale electronic devices.14 The dissociation of aryl halides
is the first mechanistic step of this reaction, however the process
only occurs under ultra-high vacuum and at high
temperatures.15
RESULTS AND DISCUSSION
Conductance measurements were carried out using the
scanning tunneling microscope-based break junction (STM-BJ)
technique2,4 using solutions of the molecules in 1,2,4-
trichlorobenzene (TCB, a non-polar solvent) or propylene
carbonate (PC, a polar solvent). For the PC measurements, the
Au tip was coated with an insulating layer to suppress
background ionic current.16 One dimensional (1D) conductance
histograms and two-dimensional (2D) conductance-
displacement histograms are constructed by compiling
thousands of traces into logarithmic (conductance) and linear
(displacement) bins without any data selection (see SI for
details).
We first examine molecules in the series 1-4 comprising 1-4
phenylene units with asymmetric thiomethyl and iodide
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Figure 1. (a) Schematic of a single molecule junction and structure of 1-4. (b) Logarithm-binned 1D histogram of 3 showing two peaks (taken
at 100 mV in TCB). The histogram is fit with a double Gaussian (red), which is divided into high-G (magenta) and low-G (green) constituents.
(c) Individual traces demonstrating the different conductance values corresponding to the high-G and low-G peaks.
linkers (Figure 1a). These molecules were synthesized using an
iterative Suzuki cross-coupling strategy followed by functional
group modification (see SI for synthetic details). The
asymmetry of the linkers allows us to specifically probe the
behavior of the iodide. Figure 1b highlights conductance data
taken in TCB at 100 mV for 3 (see Figure S2 for the complete
series). At all biases, there are two conductance states,
suggesting the presence of two binding modes. The distinct
conductance signatures are evidenced by a double peak in the
1D histogram (Figure 1b), and two plateaus of similar lengths
in the individual traces (Figure 1c). The high- and low-
conductance values (high- and low-G, respectively), extracted
from the 1D histogram by fitting with a double Gaussian to
these data, are 2.510–4 and 1.010–3 G0 for 3. Analogous
analyses for 1, 2 and 4 are in Figure S2.
junctions analogous to those created with 1-3 upon AuC bond
formation. We first discuss Au3 in relation to 3 (Figure 2c-e),
and note that our observations apply to the complete series
(Figure S4). Conductance measurements on Au3, performed
under the same conditions as 3, reveal only one conductance
state whose position aligns with the high-G peak of 3. The
conductance value for Au3, obtained from a Gaussian fit of the
peak, is in good agreement with the high-G of 3 (Figure 2c).
Moreover, the conductance plateau of Au3 in the 2D histogram
(Figure 2e) has essentially the same shape and position as the
high-G plateau of 3 (Figure 2d). We note that the plateau length
of Au3 is slightly longer than that of 3, likely due to the extra
Au atom (Figure S4 for entire series), as has been previously
observed in analogous measurements.19 These observations
strongly support that Au3 and the high-G conductance state of
3 are the same molecule in the junction.
These two different conductance states are remarkable, and
cannot be attributed to two molecules in parallel given the factor
of ~4 difference in conductance. Since we predominantly see
either the high-G or the low-G, we can also rule out a simple
junction conformational change that occurs upon elongation
seen for analogous backbones with pyridine terminations.17 We
therefore hypothesize that the two conductance states arise from
two distinct binding modes of the molecule in the junction: the
low-G peak corresponds to molecules binding through a dative
AuI bond, and the high-G peak to molecules binding through
a covalent AuC bond, which forms through an oxidative
addition of the aryl iodide to an undercoordinated Au atom at
the electrode surface (Figure 2a). This hypothesis also
rationalizes our observation that for each molecule, the length
of the plateaus is consistent with the molecular length. We
ascribe the low-G component of the double Gaussian fit to the
AuI interaction (Figure 1b, green) and the high-G component
to the AuC interaction (magenta). The dative AuI interaction
leads to a wider distribution of conductance values due to the
many possible binding geometries and increased degrees of
freedom of the arylIAu contact. Symmetric molecules with
two iodide linkers were also studied (Figure S3), but these yield
more complicated data due to the multiple possible
combinations of iodide dissociation.
The conductance values determined from both series, 1-4 and
Au1-Au3, are plotted as a function of the molecular length
(expressed as the number of phenylene units) on a semi-
logarithmic scale (Figure 2f). From a linear fit of this data, we
obtain the slope , where G ~ e-n describing the exponential
decay of conductance with increasing number of phenylene
units. The low-G state of 1-4 has a  value of 1.5 per phenylene
unit, in good agreement with oligophenylene systems with
dative linkers20,21. The  value for the high-G state of 1-4 is
close to that of the Au1-Au3 series and is smaller (1.2 per
phenylene unit). This reinforces our conclusion that two distinct
types of binding are occurring. Together, these observations
confirm our hypothesis that the iodide dissociates in the
junction, and a higher-conducting covalent AuC linkage forms
via oxidative addition. We theorize that the undercoordinated
Au atoms at the junction, which are electron rich and reactive,
promote the dissociation of the iodide by transferring electron
density to the aryl carbon, enabling the formation the AuC
bond.
To understand these results, we turn to DFT to model the
transmission across the molecular junctions using the FHI-aims
package22,23 and the AITRANSS code.24,25 The modeled
molecule in the junction is bound to the apex atoms of two 60-
atom tetrahedral Au clusters that represent the electrodes. The
transmission functions for 1-4 and Au1-Au4 are calculated
using the non-equilibrium Green's function formalism24,25
starting from junction geometries optimized using the PBE
exchange-correlation functional26 (Figure 3a). The calculated
molecular junction conductance of 2-4, which is proportional
To substantiate this hypothesis, we synthesized a new series
of molecules (see SI for synthetic details) with an intrinsic
AuC bond in which the iodide linker present in 1-3 is replaced
by a AuI(PPh3) complex (Figure 2b, Au1-Au3).11,18 Based on
the propensity of the PPh3 ligand to dissociate from the Au atom
in the junction,8 we conclude that Au1-Au3 form molecular
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Figure 2. (a) Schematic of oxidative addition in the junction. (b) Structure of Au1-Au3. (c) 1D histograms of 3 (blue) and Au3 (yellow). The
black dashed line is a guide for the eye denoting the high-G conductance value of 3, and aligning with the peak conductance value for Au3.
(d) 2D histogram of 3 (TCB, 100 mV), with the black dashed line denoting the high-G conductance value. (e) 2D histogram of Au3 (TCB,
100 mV), with the same black dashed line denoting the 3 high-G conductance value aligning with the Au3 peak conductance. The longer
plateau is consistent with an extra Au atom in the junction. (f) Semi-logarithmic plot of the conductance histogram peak value as a function
of the number of phenylene units in the backbone of 1-4 (filled circles) and Au1-Au3 (unfilled diamonds). The Au1-Au3 peak values align
with the high-G values of 1-4.  values are calculated from the linear fit.
to the transmission at the Fermi level (EF), is lower than that of
Au2-Au4, with the difference in conductance increasing with
molecular length. This trend reproduces the experimental
results shown in Figure 2f. Figure 3b shows the transmission at
EF of 1-4 and Au1-Au4 plotted against molecule length. This
data is fit to an exponential function T = Aeβn to obtain the
conductance decay for the series. The β value obtained from the
fit of the 1-4 series (0.69 per phenylene unit) is larger than that
of the Au1-Au4 series (0.58 per phenylene unit), also in
agreement with the experimental observations (Figure 3b).
These calculations provide further support to our hypothesis
that the iodide dissociates during junction formation resulting
in an Auaryl linkage.
The DFT-based calculations discussed above overestimate
the conductance27 because the PBE exchange-correlation
functional underestimates the molecular HOMO-LUMO gaps.
To examine this limitation, we repeated the calculation using
B3LYP functional, which yields more accurate HOMO-LUMO
gaps but is computationally expensive. We modeled 2 and Au2
attached to 18 Au atom clusters as model electrodes and find
that for both junctions, the HOMO-LUMO gap is larger and the
transmission at EF calculated using the B3LYP functional is
lower than those calculated using PBE (Figure S5).28–30 Note
that DFT does not include the polarizability of metal in response
to charge transfer, implying that B3LYP overestimates the
energy separation between the HOMO and LUMO resonances
in
Figure 3. (a) Calculated transmission functions of 1-4 and Au1-Au4. (b) Calculated transmission at EF plotted against molecule length,
demonstrating the decay is different for each series (1-4: β = 0.69 per phenylene unit; Au1-Au4: β = 0.58 per phenylene unit).
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Figure 4. (a) Schematic of a single-molecule junction created in an ionic environment, using a wax-coated tip. When a positive tip bias is
applied (right, denoted by δ+), Au–I linkages are favored. When a negative tip bias is applied (left, denoted by δ–), electron density at the
tip can be donated to the aryl carbon, favoring the direct Au–C linkage. (b) 1D histograms taken in PC at ± 500 mV, demonstrating preferential
Au–C junction formation at negative bias. Inset: percentage of junctions that are Au–C compared to Au–I.
the transmission function.31 We may thus regard the PBE and
oxidative addition with the aryl iodide moiety to form the AuC
B3LYP results as upper and lower bounds of the transmission
function, respectively. The transmission of Au2 is about two-
fold higher than 2 at EF according to PBE and ten-fold
according to B3LYP. This again fits the experimental trends.
When measured in TCB, the 1D and 2D histograms of 1-4
consistently show conductance features indicative of both
dative AuI and covalent AuC linkages. We now demonstrate
that the formation of the AuC linkage can be actively favored
by using an electrical bias to modulate the chemical potential of
the electrode. These measurements are performed with a wax-
coated tip in the polar solvent PC with tetrabutylammonium
hexafluorophosphate (TBAPF6, 100 mM concentration) as a
supporting electrolyte. This setup allows us to polarize the tip
electrode through the formation of a dense double layer of
charge at the small exposed area.32 Figure 4a illustrates how the
application of a negative bias increases the chemical potential
of the tip, making it electron rich, therefore promoting the
oxidative addition reaction that leads to the AuC bond
formation.
bond.
CONCLUSION
By studying a series of asymmetric oligophenylene
compounds, we have established two different binding modes
of aryl iodide linkers to Au electrodes in single-molecule
junctions. We observe both a lower-conducting, dative Au–I
contact and a higher-conducting, covalent Au–C bond. Our data
indicate that the Au–C bond forms through an oxidative
addition process, in which the electron rich Au electrode
enables iodide dissociation. Remarkably, this reaction can be
controlled by the applied tip bias. This leads to desirable,
higher-conducting covalent Au–C linkages that were previously
accessible only through complicated methods. This work opens
the door to manipulating chemical transformations using the
electric field generated in the molecular junction.
ASSOCIATED CONTENT
Supporting Information
To examine this possibility, we measured 3 at various applied
tip biases between –500 and 500 mV. All 1D histograms show
both low-G and high-G peaks (Figure S6), indicating that both
AuI and AuC bound junctions form. The relative height of
these two peaks, however, changes dramatically with bias. This
is illustrated in Figure 4b for tip biases of –500 and 500 mV.
Note that the peaks shift as a result of the applied bias due to a
gating effect.33 At 500 mV, the height of the two peaks is
similar, signifying that both AuI and AuC bound junctions
are equally probable. At –500 mV the high-G peak is much
more prominent, demonstrating that AuC bound junctions
form much more frequently than AuI bound ones at negative
bias.
To quantify the effect of the applied bias, we analyze our
traces to determine the percentage of high-G traces in a given
data set (Figure S6). The average percentage of high-G at each
bias is shown in the inset of Figure 4b. The percentage of high-
G traces gradually increases as the bias changes from 500 to –
500 mV, essentially doubling from around 40% to 80% within
this bias range. At positive bias, the tip is electron deficient, and
both AuI and AuC interactions are present while at negative
bias, the tip is electron rich and thus more prone to undergo
The Supporting Information is available free of charge on the ACS
Publications website.
Synthetic details, characterization, DFT calculations, STM-BJ
experimental details, and additional data (PDF)
AUTHOR INFORMATION
Corresponding Authors
lv2117@columbia.edu
xr2114@columbia.edu
Author Contributions
The manuscript was written through contributions of all authors.
All authors have given approval to the final version of the
manuscript.
ACKNOWLEDGMENTS
Experimental work was supported primarily by the National
Science Foundation award grant CHE-1807654 and CAREER
Award DMR-1751949. T.F. is supported by the NSF Graduate
Research Fellowship under grant CHE-1764256. We thank María
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Characterization of STM Tips for Electrochemical Studies. Rev. Sci.
Instrum. 1989, 60 (10), 3128–3130.
(17) Quek, S. Y.; Kamenetska, M.; Steigerwald, M. L.; Choi, H. J.; Louie,
S. G.; Hybertsen, M. S.; Neaton, J. B.; Venkataraman, L. Mechanically
Controlled Binary Conductance Switching of a Single-Molecule Junction.
Nat. Nanotechnol. 2009, 4, 230–234.
Camarasa-Gómez and Ferdinand Evers for assistance with DFT
calculations. Mass spectrometry was carried out by Brandon
Fowler, and cyclic voltammetry by Jake Russell.
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3
REFERENCES
4
5
6
7
8
9
(1) Reed, M. A.; Zhou, C.; Muller, C. J.; Burgin, T. P.; Tour, J. M.
Conductance of a Molecular Junction. Science. 1997, 278, 252–255.
(2) Xu, B.; Tao, N. J. Measurement of Single-Molecule Resistance by
Repeated Formation of Molecular Junctions. Science. 2003, 301, 1221–
1224.
(3) Park, Y. S.; Whalley, A. C.; Kamenetska, M.; Steigerwald, M. L.;
Hybertsen, M. S.; Nuckolls, C.; Venkataraman, L. Contact Chemistry and
Single-Molecule Conductanceꢀ: A Comparison of Phosphines , Methyl
Sulfides , and Amines. J. Am. Chem. Soc. 2007, 129, 15768–15769.
(4) Venkataraman, L.; Klare, J. E.; Nuckolls, C.; Hybertsen, M. S.;
Steigerwald, M. L. Dependence of Single-Molecule Junction Conductance
on Molecular Conformation. Nature 2006, 442, 904–907.
(5) Komoto, Y.; Fujii, S.; Hara, K.; Kiguchi, M. Single Molecular
Bridging of Au Nanogap Using Aryl Halide Molecules. J. Phys. Chem. C
2013, 117, 24277–24282.
(6) Peng, L.; Huang, B.; Zou, Q.; Hong, Z.; Zheng, J.; Shao, Y.; Niu, Z.;
Zhou, X.; Xie, H.; Chen, W. Low Tunneling Decay of Iodine-Terminated
Alkane Single-Molecule Junctions. Nanoscale Res. Lett. 2018, 13, 121–
126.
(7) Zhou, G.; Tao, N.; Asai, Y. The Orbital Selection Rule for Molecular
Conductance as Manifested in Tetraphenyl-Based Molecular Junctions. J.
Am. Chem. Soc. 2017, 139, 2989–2993.
(8) Cheng, Z.; Skouta, R.; Vazquez, H.; Widawsky, J. R.; Schneebeli, S.;
Chen, W.; Hybertsen, M. S. In Situ Formation of Highly Conducting
Covalent Au–C Contacts for Single-Molecule Junctions. Nat. Nanotechnol.
2011, 6 (6), 353–357.
(9) Hong, W.; Li, H.; Liu, S.; Fu, Y.; Li, J.; Kaliginedi, V.; Decurtins, S.;
Wandlowski, T. Trimethylsilyl-Terminated Oligo(Phenylene Ethynylene)s:
An Approach to Single-Molecule Junctions with Covalent Au−C Σ‑Bonds.
J. Am. Chem. Soc. 2012, 134 (47), 19425–19431.
(10) Bejarano, F.; Olavarria-contreras, I. J.; Droghetti, A.; Rungger, I.;
Rudnev, A.; Gutiérrez, D.; Mas-torrent, M.; Veciana, J.; van der Zant, H. S.
J.; Rovira, C.; Burzurí, E.; Crivillers, N. Robust Organic Radical Molecular
Junctions Using Acetylene Terminated Groups for C−Au Bond Formation.
J. Am. Chem. Soc. 2018, 140, 1691–1696.
(11) Millar, D.; Venkataraman, L.; Doerrer, L. H. Efficacy of Au - Au
Contacts for Scanning Tunneling Microscopy Molecular Conductance
Measurements. J. Phys. Chem. C 2007, 111 (47), 17635–17639.
(12) Batra, A.; Kladnik, G.; Gorjizadeh, N.; Steigerwald, M.; Nuckolls,
C.; Quek, S. Y.; Cvetko, D.; Morgante, A.; Venkataraman, L. Trimethyltin-
Mediated Covalent Gold − Carbon Bond Formation. J. Am. Chem. Soc.
2014, 136 (36), 12556–12559.
(13) Chen, W.; Widawsky, J. R. Highly Conducting π -Conjugated
Molecular Junctions Covalently Bonded to Gold Electrodes. J. Am. Chem.
Soc. 2011, 133 (43), 17160–17163.
(14) Cai, J.; Ruffieux, P.; Jaafar, R.; Bieri, M.; Braun, T.; Blankenburg,
S.; Muoth, M.; Seitsonen, A. P.; Saleh, M.; Feng, X.; Müllen, K.; Fasel, R.
Atomically Precise Bottom-up Fabrication of Graphene Nanoribbons. Nat.
Lett. 2010, 466, 470–473.
(15) Batra, A.; Cvetko, D.; Kladnik, G.; Adak, O.; Cardoso, C.; Ferretti,
A.; Prezzi, D.; Molinari, E.; Morgante, A.; Venkataraman, L. Probing the
Mechanism for Graphene Nanoribbon Formation on Gold Surfaces through
X-Ray Spectroscopy. Chem. Sci. 2014, 5, 4419–4423.
(18) Pankajakshan, S.; Loh, T. Base-Free Palladium-Catalyzed
Sonogashira Coupling Using Organogold Complexes. Chem. Asian J. 2011,
6, 2291–2295.
(19) Inkpen, M. S.; Liu, Z. F.; Li, H.; Campos, L. M.; Neaton, J. B.;
Venkataraman, L. Non-Chemisorbed Gold–Sulfur Binding Prevails in Self-
Assembled Monolayers. Nat. Chem. 2019, 11, 351–358.
(20) Zang, Y.; Pinkard, A.; Liu, Z.; Neaton, B.; Steigerwald, M. L.; Roy,
X.; Venkataraman, L. Electronically Transparent Au − N Bonds for
Molecular Junctions. J. Am. Chem. Soc. 2017, 139, 14845–14848.
(21) Hsu, L.; Wu, N.; Rabitz, H. Conductance and Activation Energy for
Electron Transport in Series and Parallel Intramolecular Circuits. Phys.
Chem. Chem. Phys. 2016, 18, 32087–32095.
(22) Blum, V.; Gehrke, R.; Hanke, F.; Havu, P.; Havu, V.; Ren, X.; Reuter,
K.; Scheffler, M. Ab Initio Molecular Simulations with Numeric Atom-
Centered Orbitals. Comput. Phys. Commun. 2009, 180 (11), 2175–2196.
(23) Havu, V.; Blum, V.; Havu, P.; Scheffler, M. Efficient O(N)
Integration for All-Electron Electronic Structure Calculation Using
Numeric Basis Functions. J. Comput. Phys. 2009, 228 (22), 8367–8379.
(24) Arnold, A.; Weigend, F.; Evers, F. Quantum Chemistry Calculations
for Molecules Coupled to Reservoirsꢀ: Formalism , Implementation , and
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
Application to Benzenedithiol Formalism
, Implementation , and
Application to Benzenedithiol. J. Chem. Phys. 2007, 126, 174101.
(25) Bagrets, A. Spin-Polarized Electron Transport Across Metal−Organic
Molecules: A Density Functional Theory Approach. J. Chem. Theory
Comput. 2013, 9, 2801–2815.
(26) Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient
Approximation Made Simple. Phys. Rev. Lett. 1996, 77 (18), 3865–3868.
(27) Koentopp, M.; Burke, K.; Evers, F. Zero-Bias Molecular Electronicsꢀ:
Exchange-Correlation Corrections to Landauer’s Formula. Phys. Rev. B
2006, 73, 121403.
(28) Vosko, S.; Wilk, L.; Nusair, M. Accurate Spin-Dependent Electron
Liquid Correlation Energies for Local Spin Density Calculations: A Critical
Analysis1. Can. J. Phys. 1980, 58, 1200.
(29) Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti
Correlation-Energy Formula into a Functional of the Electron Density.
Phys. Rev. B 1988, 37 (2), 785–789.
(30) Becke, A. D. A New Mixing of Hartree–Fock and Local Density-
Functional Theories. J. Chem. Phys. 1993, 98, 1372.
(31) Egger, D. A.; Liu, Z.; Kronik, L. Reliable Energy Level Alignment at
Physisorbed Molecule − Metal Interfaces from Density Functional Theory.
Nano Lett. 2015, 15, 2448–2455.
(32) Capozzi, B.; Xia, J.; Adak, O.; Dell, E. J.; Liu, Z.; Taylor, J. C.;
Neaton, J. B.; Campos, L. M.; Venkataraman, L. Single-Molecule Diodes
with High Recti Fi Cation Ratios through Environmental Control. Nat.
Nanotechnol. 2015, 10, 522–527.
(33) Capozzi, B.; Low, J. Z.; Xia, J.; Liu, Z.-F.; Neaton, J. B.; Campos, L.
M.; Venkataraman, L. Mapping the Transmission Functions of Single-
Molecule Junctions. Nano Lett. 2016, 16 (6), 3949–3954.
(16) Nagahara, L. A.; Thundat, T.; Lindsay, S. M. Preparation and
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