5 research outputs found
Understanding and Controlling the 1,4-Phenylene DiisocyanideāGold Oligomer Formation Pathways
The pathways for the spontaneous
self-assembly of one-dimensional
oligomeric chains from the adsorption of 1,4-phenylene diisocyanide
(PDI) on Au(111) surface are explored using density functional theory.
It has been shown previously that the chain comprises repeating ā(AuāPDI)ā
structures. The results show that the chains form from mobile AuāPDI
adatom complexes and that chains propagate by the adatom complex coupling
to a terminal isocyanide group which lies close to parallel to the
surface and the activation barrier for this propagation step is ā¼28
kJ/mol. It is also found that the AuāPDI adatom complex is
attracted to the terminal isocyanide, thereby facilitating the oligomerization
process. The insights into the oligomerization pathway are used to
explore whether an external electric field applied to diisocyanide
functionalized molecules that contain a dipole moment can be used
to align them. It is found that molecules with dipole moments of ā¼1
D show significant alignment with an electric field of ā¼10<sup>8</sup> V/m and almost complete alignment when the electric field
reaches ā¼10<sup>9</sup> V/m. This suggests that the self-assembly
chemistry of dipolar diisocyanides can be used to create oriented
systems
Understanding and Controlling the 1,4-Phenylene DiisocyanideāGold Oligomer Formation Pathways
The pathways for the spontaneous
self-assembly of one-dimensional
oligomeric chains from the adsorption of 1,4-phenylene diisocyanide
(PDI) on Au(111) surface are explored using density functional theory.
It has been shown previously that the chain comprises repeating ā(AuāPDI)ā
structures. The results show that the chains form from mobile AuāPDI
adatom complexes and that chains propagate by the adatom complex coupling
to a terminal isocyanide group which lies close to parallel to the
surface and the activation barrier for this propagation step is ā¼28
kJ/mol. It is also found that the AuāPDI adatom complex is
attracted to the terminal isocyanide, thereby facilitating the oligomerization
process. The insights into the oligomerization pathway are used to
explore whether an external electric field applied to diisocyanide
functionalized molecules that contain a dipole moment can be used
to align them. It is found that molecules with dipole moments of ā¼1
D show significant alignment with an electric field of ā¼10<sup>8</sup> V/m and almost complete alignment when the electric field
reaches ā¼10<sup>9</sup> V/m. This suggests that the self-assembly
chemistry of dipolar diisocyanides can be used to create oriented
systems
Structural Changes in Self-Catalyzed Adsorption of Carbon Monoxide on 1,4-Phenylene Diisocyanide Modified Au(111)
The
self-accelerated adsorption of CO on 1,4-phenylene diisocyanide
(PDI)-derived oligomers on Au(111) is explored by reflectionāabsorption
infrared spectroscopy and scanning tunneling microscopy. PDI incorporates
gold adatoms from the Au(111) surface to form one-dimensional ā(AuāPDI)<sub><i>n</i></sub>ā chains that can also connect between
gold nanoparticles on mica to form a conductive pathway between them.
CO adsorption occurs in two stages; it first adsorbs adjacent to the
oligomers that move to optimize CO adsorption. Further CO exposure
induces PDI decoordination to form AuāPDI adatom complexes
thereby causing the conductivity of a PDI-linked gold nanoparticle
array on mica to decrease to act as a chemically drive molecular switch.
This simple system enables the adsorption process to be explored in
detail. DFT calculations reveal that both the ā(AuāPDI)<sub><i>n</i></sub>ā oligomer chain and the AuāPDI
adatom complex are stabilized by coadsorbed CO. A kinetic āfoot-in-the-doorā
model is proposed in which fluctuations in PDI coordination allow
CO to diffuse into the gap between gold adatoms to prevent the PDI
from reattaching, thereby allowing additional CO to adsorb, to provide
kinetic model for allosteric CO adsorption on PDI-covered gold
Identifying Molecular Species on Surfaces by Scanning Tunneling Microscopy: Methyl Pyruvate on Pd(111)
The structures of low coverages of
methyl pyruvate on a Pd(111)
surface at 120 K were studied using scanning tunneling microscopy
in ultrahigh vacuum. The experimentally observed images were assigned
to adsorbate structures using a combination of density functional
theory calculations and by simulating the images using the Bardeen
method. Two forms of methyl pyruvate were identified. The first, previously
found using reflectionāabsorption infrared spectroscopy, was
a flat-lying, keto form of <i>cis</i>-methyl pyruvate. It
was characterized by elongated, two-lobed images with the long axes
of the images oriented at ā¼0 and ā¼30Ā° to the close-packed
directions. The structure was simulated using clean, CO- and methyl-functionalized
gold tips, and the simulated images agreed well with those found experimentally.
The simulated structures were not strongly dependent on the tip structure
or tip bias. This approach was used to identify the nature of the
second species as the enol form of <i>cis</i>-methyl pyruvate
with the carbonyl groups located over atop and bridge sites. Again,
the orientation of the image with respect to the underlying Pd(111)
lattice as well as the calculated image shape agreed well with the
experimental images
Formation of Chiral Self-Assembled Structures of Amino Acids on Transition-Metal Surfaces: Alanine on Pd(111)
The structure and self-assembly of
alanine on Pd(111) is explored using X-ray photoelectron spectroscopy
(XPS), low-energy electron diffraction (LEED), reflectionāabsorption
infrared spectroscopy (RAIRS), and scanning tunneling microscopy (STM),
and supplemented by density functional theory (DFT) calculations to
explore the stability of the proposed surface structures formed by
adsorbing alanine on Pd(111) and to simulate the STM images. Both
zwitterionic and anionic species are detected using RAIRS and XPS,
while DFT calculations indicate that isolated anionic alanine is significantly
more stable than the zwitterion. This observation is rationalized
by observing dimeric species when alanine is dosed at ā¼270
K and then cooled to trap metastable surface structures. The dimers
form due to an interaction between the carboxylate group of anionic
alanine with the NH<sub>3</sub><sup>+</sup> group of the zwitterion.
Adsorbing alanine at 290 K results in the formation of dimer rows
and tetramers resulting in only short-range order, consistent with
the lack of additional diffraction spots in LEED. The stability of
various structures is explored using DFT, and the simulated STM images
are compared with experiment. This enables the dimer rows to be assigned
to the assembly of anionic-zwitterionic dimers and the tetramer to
the assembly of two dimers in which three of the alanine molecules
undergo a concerted rotation by 30Ā°