Raman spectroscopy of molecular electronic junctions

Molecular Electronics uses molecules sandwiched between two metals as a model system to create tailored solutions for applications such as energy harvesting and sensing. Electrons tunnelling across such a junction are a↵ected by the properties of the molecule itself as well as the interaction between metal and molecule. In particular, charge transport is known to couple to molecular vibrations, which can act both to dissipate energy as well as increase conductance. This thesis therefore applies in-situ vibrational spectroscopies, surface-enhanced Raman scattering and vibrational sum frequency generation, to investigate molecular junctions. As a model system, 4-mercaptopyridine sandwiched between a gold surface and an elec- trochemically deposited second metal layer is used. Four aspects are studied in detail in this thesis. Chapter 3 presents a detailed study of surface enhanced Raman spectra of 4-mercaptopyridine on gold. All experimental vibrational modes are assigned and related to the symmetry of the adsorbed molecule with the help of density functional calculations. In particular, the e↵ect of hydrogen bonding on the ring breathing modes of adsorbed mercaptopyridine is revealed for the first time. In chapter 4, surface-enhanced Raman spectroscopy is used to identify a spectroscopic signature of a successfully formed metal-molecule-metal junction after electrochemical deposition of a tran- sition metal layer. Chapter 5 then addresses the use of surface-enhanced Raman spectroscopy to identify charge transfer states of 4-mercaptopyridine by changing bias potential and excitation wavelength. A charge transfer state is found for protonated 4-mercaptopyridine at about 1.7 eV above the Fermi level, while the corresponding state for unprotonated 4-mercaptopyridine must lie at least 0.8 eV higher. Chapter 6 then explores the use of ultrafast vibrational sum frequency generation. The pyridine ring stretching modes are detected and metallisation of the 4-mercaptopyridine layer is seen to decrease the local order of the molecular layer. The influence of the mercaptopyridine charge transfer state can be seen in ultrafast pump - sum frequency probe spectroscopy of the gold substrate. This opens the prospect of investigating coupling between molecular vibrations and charge transfer in these junctions on a timescale of a picosecond or less

Detection of metal-molecule-metal junction formation by surface enhanced Raman spectroscopy

Vibrational modes play a key role in characterizing metal-molecule-metal junctions, but their detection currently either requires single-molecule sensitivity or the generation of defect-free large-scale junctions. Here we demonstrate that surface-enhanced Raman scattering (SERS) on non-ideal surfaces can provide a significant amount of information despite many defects in the layer. We determine the vibrational signature of the molecular electronic junction for palladium ions complexed and reduced on 4-mercaptopyridine adsorbed on rough gold and gold nanoparticles using SERS and density functional theory (DFT). We show that these non-ideal surfaces can be used to probe kinetics of metal ion com-plexation and establish the success of electrochemical metallization. SERS on non-ideal surfaces is thus revealed as a useful tool to rapidly establish the key process parameters in making molecular electronic junctions before embarking on more detailed studies on single molecules or single crystal surfaces

GFP Pattern Recognition in Raman Spectra by Modified VGG Networks for Localisation Tracking in Living Cells

The coupling between Raman spectroscopy and green fluorescent protein (GFP) labelling informs chemical compositions at the specific sites. This information leading to study that explain core knowledge of living organism and eventually advance our conventional technique of medical diagnosis. In order to achieve these purposes, the precise interpretation is required. A massive number of Raman/GFP spectra as well as identification of GFP contribution in each spectrum are arroaches to achieve those goals. In the paper, CNN is proposed to classify the spectra with and without GFP signal. The dataset of GFP-positive and GFP-negative spectra were created with various size and background color. The feature extraction and classification are conduced with VGG networks. To increase the performance of VGG network, the modified VGG13 and modified VGG19 were designed. These two models extend fully-connected layer from 3 (the original VGG model) to 5 layer for better classification task. Batch normalization is also added at the end of feature extraction units to reduce unpredicted shifting of parameters. The original VGG16, VGG19, and ResNet50 are used as comparison models. The results show that both of our modified VGG models significantly enhances training accuracy of the network comparing to the original VGG. The accuracy of original VGG can be increased when applied pre-trained weight, but the accuracies are yet slightly lower than modified models. Training on ResNet, deeper network, gave the comparable accuracy with our modified models

Discrimination between hydrogen bonding and protonation in the spectra of a surface-enhanced Raman sensor

We investigate the surface-enhanced Raman spectra of 4-mercaptopyridine on gold in a variety of acids. 4-Mercaptopyridine is a known pH sensor which exhibits characteristic spectral changes when the pH is changed. Here we show with the help of experiment and density functional calculations that the ring breathing mode is also highly sensitive to hydrogen bonding. Its spectral signature is a broad band with up to three contributions from free, protonated and hydrogen-bonded 4-mercaptopyridine. Unlike pyridine in solution, where protonation leads to a higher ring breathing frequency than hydrogen-bonding, we find that protonated adsorbed 4-mercaptopyridine possesses a frequency which is lower than the corresponding hydrogen-bonded species. The Raman spectra indicate an orientation change of the aromatic ring in acidic solutions, which could be caused by a cation/π interaction between protonated and deprotonated 4-mercaptopyridine. As the frequencies of the three species are well separated, adsorbed 4-mercaptopyridine can probe more complex changes in the solution environment than just pH

Coordination controlled electrodeposition and patterning of layers of palladium/copper nanoparticles on top of a self-assembled monolayer

Support by EPSRC (EP/E061303/1, EP/D048761/1) and the Chinese Scholarship Council and the University of St Andrews for a stipend (Z. Y.) are gratefully acknowledged.A scheme for the generation of bimetallic nanoparticles is presented which combines electrodeposition of one type of metal, coordinated to a self-assembled monolayer (SAM), with another metal deposited from the bulk electrolyte. In this way PdCu nanoparticles are generated by initial complexation of Pd2+ to a SAM of 3-(4-(pyridine-4-yl)phenyl)propane-1-thiol (PyP3) on Au/mica and subsequent reduction in an acidic aqueous CuSO4 electrolyte. Cyclic voltammetry reveals that the onset of Cu deposition is triggered by Pd reduction. Scanning tunneling microscopy (STM) shows that layers of connected particles are formed with an average thickness of less than 3 nm and lateral dimensions of particles in the range of 2 to 5 nm. In X-ray photoelectron spectra a range of binding energies for the Pd 3d signal is observed whereas the Cu 2p signal appears at a single binding energy, even though chemically different Cu species are present: normal and more noble Cu. Up to three components are seen in the N 1s signal, one originating from protonated pyridine moieties, the others reflecting the SAM-metal interaction. It is suggested that the coordination controlled electrodeposition yields layers of particles composed of a Pd core and a Cu shell with a transition region of a PdCu alloy. Deposited on top of the PyP3 SAM, the PdCu particles exhibit weak adhesion which is exploited for patterning by selective removal of particles employing scanning probe techniques. The potential for patterning down to the sub-10 nm scale is demonstrated. Harnessing the deposition contrast between native and PdCu loaded PyP3 SAMs, structures thus created can be developed into patterned continuous layers.PostprintPeer reviewe

Mitochondria specific Raman microspectroscopy of fission yeast cells with simultaneous Raman/GFP observation

Mitochondria are one of the crucial organelles that maintain cell living status. Many researches have been carried out on mitochondria to gain more knowledge about life. Here, we report the first mitochondria specific Raman spectra of fission yeast, Schizosaccharomyces pombe, using a novel bio-spectroscopic technique, “simultaneous Raman/GFP microspectroscopy”.Published versio

Microbial Poly(hydroxybutyrate-co-hydroxyvalerate) Scaffold for Periodontal Tissue Engineering

In this study, we fabricated three dimensional (3D) porous scaffolds of poly(hydroxybutyrate-co-hydroxyvalerate) with 50% HV content. P(HB-50HV) was biosynthesized from bacteria Cupriavidus necator H16 and the in vitro proliferation of dental cells for tissue engineering application was evaluated. Comparisons were made with scaffolds prepared by poly(hydroxybutyrate) (PHB), poly(hydroxybutyrate-co-12%hydroxyvalerate) (P(HB-12HV)), and polycaprolactone (PCL). The water contact angle results indicated a hydrophobic character for all polymeric films. All fabricated scaffolds exhibited a high porosity of 90% with a sponge-like appearance. The P(HB-50HV) scaffolds were distinctively different in compressive modulus and was the material with the lowest stiffness among all scaffolds tested between the dry and wet conditions. The human gingival fibroblasts (HGFs) and periodontal ligament stem cells (PDLSCs) cultured onto the P(HB-50HV) scaffold adhered to the scaffold and exhibited the highest proliferation with a healthy morphology, demonstrating excellent cell compatibility with P(HB-50HV) scaffolds. These results indicate that the P(HB-50HV) scaffold could be applied as a biomaterial for periodontal tissue engineering and stem cell applications

Microbial Poly(hydroxybutyrate-co-hydroxyvalerate) Scaffold for Periodontal Tissue Engineering

In this study, we fabricated three dimensional (3D) porous scaffolds of poly(hydroxybutyrate-co-hydroxyvalerate) with 50% HV content. P(HB-50HV) was biosynthesized from bacteria Cupriavidus necator H16 and the in vitro proliferation of dental cells for tissue engineering application was evaluated. Comparisons were made with scaffolds prepared by poly(hydroxybutyrate) (PHB), poly(hydroxybutyrate-co-12%hydroxyvalerate) (P(HB-12HV)), and polycaprolactone (PCL). The water contact angle results indicated a hydrophobic character for all polymeric films. All fabricated scaffolds exhibited a high porosity of 90% with a sponge-like appearance. The P(HB-50HV) scaffolds were distinctively different in compressive modulus and was the material with the lowest stiffness among all scaffolds tested between the dry and wet conditions. The human gingival fibroblasts (HGFs) and periodontal ligament stem cells (PDLSCs) cultured onto the P(HB-50HV) scaffold adhered to the scaffold and exhibited the highest proliferation with a healthy morphology, demonstrating excellent cell compatibility with P(HB-50HV) scaffolds. These results indicate that the P(HB-50HV) scaffold could be applied as a biomaterial for periodontal tissue engineering and stem cell applications