Physical Sciences and Mathematics Commons^™

Solvent Stable Microbial Lipases: Current Understanding And Biotechnological Applications, Barry Ryan, Priyanka Priyanka, Yeqi Tan, Gemma K Kinsella, Gary T. Henehan

Articles

Objective: This review examines on our current understanding of microbial lipase solvent tolerance, with a specific focus on the molecular strategies employed to improve lipase stability in a non-aqueous environment.

Results: It provides an overview of known solvent tolerant lipases and of approaches to improving solvent stability such as; enhancing stabilising interactions, modification of residue flexibility and surface charge alteration. It shows that judicious selection of lipase source supplemented by appropriate enzyme stabilisation, can lead to a wide application spectrum for lipases.

Conclusion: Organic solvent stable lipases are, and will continue to be, versatile and adaptable biocatalytic workhorses commonly employed …

On The Exactitude Of Big Data: La Bêtise And Artificial Intelligence, Noel Fitzpatrick, John D. Kelleher

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This article revisits the question of ‘la bêtise’ or stupidity in the era of Artificial Intelligence driven by Big Data, it extends on the questions posed by Gille Deleuze and more recently by Bernard Stiegler. However, the framework for revisiting the question of la bêtise will be through the lens of contemporary computer science, in particular the development of data science as a mode of analysis, sometimes, misinterpreted as a mode of intelligence. In particular, this article will argue that with the advent of forms of hype (sometimes referred to as the hype cycle) in relation to big data and …

Regeneration Of Aged Dmf For Use In Solid-Phase Peptide Synthesis, Jordan K. Magtaan, Marc Devocelle, Fintan Kelleher

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DMF, which is still the most commonly used solvent for Fmoc-SPPS, has the potential for degradation over time on exposure to air (and water vapour) and storage, to give dimethylamine and formic acid impurities. In particular, dimethylamine can lead to unwanted deprotection of the Fmoc group during for example the initial loading of Fmoc amino acids in SPPS, which leads reduced calculated loading values. We have found that treatment of such aged DMF by simple sparging with an inert gas (N₂), or vacuum sonication, can regenerate the DMF in order to restore loading levels back to those found …

Exchanging Personal Health Data With Electronic Health Records: A Standardized Information Model For Patient Generated Health Data And Observations Of Daily Living, Panagiotis Plastiras, Dympna O'Sullivan

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Objective: The development of a middleware information model to facilitate better interoperability between Personal and Electronic Health Record systems in order to allow exchange of Patient Generated Health Data and Observations of Daily Leaving between patients and providers in order to encourage patient self-management.

Materials and methods: An information model based on HL7 standards for interoperability has been extended to support PGHD and ODL data types. The new information models uses HL7 CDA to represent data, is instantiated as a Protégé ontology and uses a set of mapping rules to transfer data between Personal and Electronic Health Record …

Raman Spectroscopy Detects Biochemical Changes Due To Different Cell Culture Environments In Live Cells In Vitro, Mahmoud Gargotti, Esen Efeoglu, Hugh Byrne, Alan Casey

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The in vitro cell culture environment can impact on cell biochemistry and cell cycle. The manifestation of such substrate-induced changes in cell cycle in the Raman microspectroscopic profiles of cell cultures is investigated at the level of nucleolus, nucleus and cytoplasm. HeLa immortalised human cervical cells and HaCaT dermal cells were cultured on three different substrates, conventional polystyrene cell culture dishes, CaF2 slides as a commonly used Raman substrate, and glass slides coated with Collagen Rat Tail, as a mimic of the extra cellular matrix (ECM) environment. A cell cycle study, based on percentage DNA content, as determined using Propidium …

Significance Of A Non-Thermal Plasma Treatment On Ldpe Biodegradation With Pseudomonas Aeruginosa, Laurence Scally, Miroslav Gulan, Lars Weigang, Patrick Cullen, Vladimir Milosavljevic

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The use of plastics has spanned across almost all aspects of day to day life. Although their uses are invaluable, they contribute to the generation of a lot of waste products that end up in the environment and end up polluting natural habitats such as forests and the ocean. By treating low-density polyethylene (LDPE) samples with non-thermal plasma in ambient air and with an addition of 4% CO2, the biodegradation of the samples can be increased due to an increase in oxidative species causing better cell adhesion and acceptance on the polymer sample surface. It was, however, found that the …

Ideating Mobile Health Behavioral Support For Compliance To Therapy For Patients With Chronic Disease: A Case Study Of Atrial Fibrillation Management, Mor Peleg, Wojtek Michalowski, Szymon Wilk, Enea Parimbelli, Silvia Bonaccio, Dympna O'Sullivan, Martin Michalowski, Silvana Quaglini, Marc Carrier

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Poor patient compliance to therapy results in a worsening condition that often increases healthcare costs. In the MobiGuide project, we developed an evidence-based clinical decision-support system that delivered personalized reminders and recommendations to patients, helping to achieve higher therapy compliance. Yet compliance could still be improved and therefore building on the MobiGuide project experience, we designed a new component called the Motivational Patient Assistant (MPA) that is integrated within the MobiGuide architecture to further improve compliance. This component draws from psychological theories to provide behavioral support to improve patient engagement and thereby increasing patients' compliance. Behavior modification interventions are delivered …

Serialised Holography For Brand Protection And Authentication, Dinesh Vather, Izabela Naydenova, Dervil Cody, Monika Zawadzka, Suzanne Martin, Emilia Mihaylova, Stephen Curran, Paul Duffy, Josune Portillo, Daniel Connell, Stephen Mcdonnell, Vincent Toal

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The problems presented by counterfeit products and documentation are discussed. Limitations of existing holograms for anti-counterfeit applications are described. We describe the advantages of full holographic serialisation and the requirements in terms of materials and techniques for mass production of true serialised holograms. These requirements having been met, we report for the first time the mass production of fully serialised holograms. The novelty of approach consists of the direct use of product manufacturer’s information as the object in a holographic recording system along with a self-processing photopolymer and modular optical system to facilitate mass production of truly serialised volume holograms. …

Performance Comparison Of Support Vector Machine, Random Forest, And Extreme Learning Machine For Intrusion Detection, Iftikhar Ahmad, Muhammad Javed Iqbal, Mohammad Basheri, Aneel Rahim

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Intrusion detection is a fundamental part of security tools, such as adaptive security appliances, intrusion detection systems, intrusion prevention systems, and firewalls. Various intrusion detection techniques are used, but their performance is an issue. Intrusion detection performance depends on accuracy, which needs to improve to decrease false alarms and to increase the detection rate. To resolve concerns on performance, multilayer perceptron, support vector machine (SVM), and other techniques have been used in recent work. Such techniques indicate limitations and are not efficient for use in large data sets, such as system and network data. The intrusion detection system is used …

Safety Implications Of Plasma-Induced Effects In Living Cells – A Review Of In Vitro And In Vivo Findings, Daniela Boehm, Paula Bourke

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Cold atmospheric plasma is a versatile new tool in the biomedical field with applications ranging from disinfection, wound healing and tissue regeneration to blood coagulation, and cancer treatment. Along with improved insights into the underlying physical, chemical and biological principles, plasma medicine has also made important advances in the introduction into the clinic. However, in the absence of a standard plasma ‘dose’ definition, the diversity of the field poses certain difficulties in terms of comparability of plasma devices, treatment parameters and resulting biological effects, particularly with regards to the question of what constitutes a safe plasma application. Data from various …

Advancing Raman Microspectroscopy For Cellular And Subcellular Analysis: Towards In Vitro High Content Spectralomic Analysis, Hugh Byrne, Franck Bonnier, Alan Casey, Marcus Maher, Jennifer Mcintyre, Esen Efeoglu, Zeineb Farhane

Articles

In the confocal mode, Raman microspectroscopy can profile the biochemical content of biological cells at a subcellular level, and any changes to it by exogenous agents, such as therapeutic drugs or toxicants. As an exploration of the potential of the technique as a high content, label free analysis technique, this report reviews work to monitor the spectroscopic signatures associated with the uptake and response pathways of commercial chemotherapeutic agents and polymeric nanoparticles by human lung cells. It is demonstrated that the signatures are reproducible and characteristic of the cellular event, and can be used, for example, to identify the mode …

Multicomponent Analysis Using A Confocal Raman Microscope, Zhengyuan Tang, Sinead J. Barton, Thomas E. Ward, John P. Lowry, Michelle M. Doran, Hugh Byrne, Bryan M. Hennelly

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Measuring the concentration of multiple chemical components in a low volume aqueous mixture by Raman spectroscopy has received significant interest in the literature. All of the contributions to date focus on the design of optical systems that facilitate the recording of spectra with high signal-to-noise ratio, by collecting as many Raman scattered photons as possible. In this study, the confocal Raman microscope set-up is investigated for multicomponent analysis. Partial Least Squares Regression is used to quantify physiologically relevant aqueous mixtures of glucose, lactic acid, and urea. The predicted error is 17.81 mg/dL for glucose, 10.6 mg/dL for lactic acid and …

Raman Spectral Analysis For Rapid Screening Of Dengue Infection, Tahir Mahmood, Haq Nawaz, A. Ditta, M.I. Majeed, M.A. Hanif, N. Rashid, H.N. Bhatti, H.F. Nargis, M. Saleem, Franck Bonnier, Hugh Byrne

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Infection with the dengue virus is currently clinically detected according to different biomarkers in human blood plasma, commonly measured by enzyme linked immunosorbent assays, including non-structural proteins (Ns1), immunoglobulin M (IgM) and immunoglobulin G (IgG). However, there is little or no mutual correlation between the biomarkers, as demonstrated in this study by a comparison of their levels in samples from 17 patients. As an alternative, the label free, rapid screening technique, Raman spectroscopy has been used for the characterisation/diagnosis of healthy and dengue infected human blood plasma samples. In dengue positive samples, changes in specific Raman spectral bands associated with …

Endoscopic Ultrasound Features Of Multiple Endocrine Neoplasia Type 1-Related Versus Sporadic Pancreatic Neuroendocrine Tumors: A Single-Center Retrospective Study, Gianluca Tamagno, Vanessa Scherer, Alberto Caimo, Simona Bergmann, Peter Kann

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Pancreatic neuroendocrine tumors (pNETs) can occur in patients with a familial syndrome either as multiple endocrine neoplasia type 1 (MEN-1) or as sporadic tumors. Endoscopic ultrasound (EUS) has become one of the first-line investigations for pNET characterization. The ultrasonographic features of pNETs may differ depending on the familial versus sporadic pathogenesis of the tumor. Therefore, the EUS findings could help and direct the definition of a pNET with an impact on the most appropriate diagnostic and ther- apeutic patient management. Methods: In this single-center retrospective study, we reviewed the EUS features of 94 pNETs from 37 MEN-1 patients and 15 …

Conformational Studies Of Gram-Negative Bacterial Quorum Sensing Acyl Homoserine Lactone (Ahl) Molecules: The Importance Of The N→* Interaction, Fintan Kelleher, Goar Sánchez-Sanz, Darren Crowe, Alan Nicholson, Adrienne Fleming

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A ¹H NMR study shows the presence of intermolecular hydrogen bonds for AHLs in CDCl₃ solution. A detailed computational study of the structure of AHLs and the relative stability between the extended conformations (X) and those showing n→p* interactions (np) have been carried out by means of DFT calculations. Solvent effects have been shown to be very important when stabilising np conformations, particularly with polar solvents. This was shown by the shortening of C···O intramolecular distances and the increase in the relative energies favouring the np conformation with the dielectric constant of the solvent. …

Holographic Beam-Shaping Diffractive Diffusers Fabricated By Using Controlled Laser Speckle, Kevin Murphy, Vincent Toal, Izabela Naydenova, Suzanne Martin

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A method for fabricating diffractive holographic optical diffusers is reported, allowing a high degree of control of the resulting diffuser characteristics. The method consists of recording a laser speckle pattern using a single carrier beam, with controlled speckle size and shape, in an acrylamide-based volume photopolymer. The multiple interferences that create the speckle pattern form the hologram. Results are presented verifying the diffusers are volume holographic in nature and the speckle pattern is recorded accurately in the photopolymer. Diffusers recorded by this method are analysed to characterise the optical performance of the diffusers and to illustrate their beam-shaping capabilities, particularly …

Investigating Secondary Students Beliefs About Mathematical Problem-Solving, Mark Prendergast, Cormac Breen, Aibhin Bray, Fiona Faulkner, Brian Carroll, Dominic Quinn

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Many studies over the past thirty years have highlighted the important role of students’ beliefs for successful problem solving in mathematics. Given the recent emphasis afforded to problem solving on the reformed Irish secondary school mathematics curriculum, the main aim of this study was to identify Irish students’ (n = 975) beliefs about the field. A quantitative measure of these beliefs was attained through the use of the Indiana Mathematical Belief Scale, an existing thirty item (five scale) self-report questionnaire. A statistical analysis of the data revealed that students who were further through their secondary education had a stronger belief …

Studies Of Geometrical Profiling In Fabricated Tapered Optical Fbers Using Whispering Gallery Modes Spectroscopy, Vishnu Kavungal, Gerald Farrell, Qiang Wu, Arun Kumar Mallik, Yuliya Semenova

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This paper experimentally demonstrates a method for geometrical profiling of asymmetries in fabricated thin microfiber tapers with waist diameters ranging from ∼10 to ∼50µm with submicron accuracy. The method is based on the analysis of whispering gallery mode resonances excited in cylindrical fiber resonators as a result of evanescent coupling of light propagating through the fiber taper. The submicron accuracy of the proposed method has been verified by SEM studies. The method can be applied as a quality control tool in fabrication of microfiber based devices and sensors or for fine-tuning of microfiber fabrication set-ups.

In Vitro Label Free Screening Of Chemotherapeutic Drugs Using Raman Micro-Spectroscopy: Towards A New Paradigm Of Spectralomics., Zeineb Farhane, Haq Nawaz, Franck Bonnier, Hugh Byrne

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This overview groups some of the recent studies highlighting the potential application of Raman micro-spectroscopy as an analytical technique in preclinical development to predict drug mechanism of action and in clinical application as a companion diagnostic and in personalised therapy due to its capacity to predict cellular resistance and therefore to optimise chemotherapeutic treatment efficacy.

Notably, the anthracyclines, Doxorubicin and Actinomycin D, elicit similar spectroscopic signatures of subcellular interaction characteristic of the mode of action of intercalation. Although Cisplatin and Vincristine show markedly different signatures, at low exposure doses, their signatures at higher doses show marked similarities to those elicited …

Confocal Raman Spectroscopic Imaging For In Vitro Monitoring Of Active Ingredient Penetration And Distribution In Reconstructed Human Epidermis Model, Lynda Miloudi, Franck Bonnier, Ali Tfayli, Florent Yvergnaux, Hugh Byrne, Igor Chourpa, Emilie Munnier

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Topically applied Active Cosmetic Ingredients (ACI) or Active Pharmaceutical Ingredients (API) efficacy is directly related to their efficiency of penetration in the skin. In vitro Reconstructed Human Epidermis (RHE) surrogate models offer in vivo like skin samples for transdermal studies. Using Delipidol®, an ACI currently used in the cosmetics industry, the capabilities to deliver accurate distribution maps and penetration profiles of this molecule by means of Confocal Raman spectroscopic Imaging have been demonstrated. Using a NCLS (Non negative constrained least squares) approach, contribution of specific molecules can be estimated at each point of spectral maps in order to deliver semi-quantitative …

Comparison Of Fungal Spores Concentrations Measured With Wideband Integrated Bioaerosol Sensor And Hirst Methodology, S. Fernández-Rodríguez, R. Tormo-Molina, N. Lemonis, B. Clot, David O'Connor, John R. Sodeau

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The aim of this work was to provide both a comparison of traditional and novel methodologies for airborne spores detection (i.e. the Hirst Burkard trap and WIBS-4) and the first quantitative study of airborne fungal concentrations in Payerne (Western Switzerland) as well as their relation to meteorological parameters. From the traditional method -Hirst trap and microscope analysis-, sixty-three propagule types (spores, sporangia and hyphae) were identified and the average spore concentrations measured over the full period amounted to 4145 ± 263.0 spores/m3. Maximum values were reached on July 19th and on August 6th. Twenty-six spore types reached average levels above …

The Janus-Faced Chromophore: A Donor-Acceptor Dyad With Dual Performance In Photon Up-Conversion, Natalia Kiseleva, Mikhail Filatov, Michael Oldenburg, Dimitry Busko, Marius Jakoby, Ian Howard, Bryce Richards, Mathias Senge, Sergey Borisov, Andrey Turshatov

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An electron donor-acceptor dyad based on BODIPY (acceptor) and anthracene (donor) plays either the role of sensitizer or emitter in triplet-triplet annihilation photon up-conversion (TTA-UC). This Janus-like behavior was achieved via altering the relative ordering of charge-transfer and local excited state energies in the dyad through the polarity of TTA-UC media.

High Sensitivity Temperature Sensor Based On Singlemode-No-Core- Singlemode Fibre Structure And Alcohol, Ke Tiana, Gerald Farrell, Xianfan Wang, Yifan Xin, Yanqiu Du, Wenlei Yang, Haidong Liang, Elfed Lewis, Pengfei Wang

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A high sensitivity temperature sensor based on a singlemode-no-core-singlemode (SNCS) fibre structure and surrounded with alcohol within a silica capillary is described. In this investigation, no-core fibre (NCF) is used as the multimode waveguide and alcohol is chosen as the temperature sensitive medium. By packaging the alcohol solution with a short length of NCF enclosed within a silica capillary, the surrounding temperature can be detected by monitoring the variations of transmission loss at a specific wavelength. The theoretical analysis predicts this temperature sensor can provide high sensitivity, and the experimental results support this. The maximum temperature sensitivity of the sample …

Nano–Bio Interactions: Nanomedicine And Nanotoxicology, Hugh Byrne, S. Mukherjee, Pratap C. Naha

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The 21st century has truly become the age of nanotechnology. Nanomaterials, design strategies, and processing have already made a significant impact in areas of materials science and electronics, with many commercial applications already being available on the consumer market. However, the ability to manipulate material functions and interactions on a scale of tens of nanometers, e.g., biological subcellular organelles, may yet prove to have the most significant impact on human health and the environment.

Self-Processing Photopolymer Materials For Versatile Design And Fabrication Of Holographic Sensors And Interactive Holograms, Dervil Cody, Sabad-E Gul, Tatsiana Mikulchyk, Muhammad Irfan, Anastasia Kharchenko, Kamila Goldyn, Suzanne Martin, Svetlana Mintova, John Cassidy, Izabela Naydenova

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The aim of this paper is to discuss the benefits as well as the limitations of utilizing photopolymer materials in the design of holograms that are responsive to changes in their environment, such as changes in the concentration of a specific substance, temperature, and pressure. Three different case studies are presented, including both surface and volume phase holograms, in order to demonstrate the flexibility in the approach of utilizing holographic photopolymers for the design of sensors and interactive optical devices. First, a functionalized surface relief hologram is demonstrated to operate as an optical sensor for the detection of metal ions …

Theoretical Modeling And Design Of Photonic Structures In Zeolite Nanocomposites For Gas Sensing. Part Ii: Volume Gratings, Dervil Cody, Izabela Naydenova

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The suitability of holographic structures fabricated in zeolite nanoparticle-polymer composite materials for gas sensing applications has been investigated. Theoretical modelling of the sensor response (i.e. change in hologram readout due to a change in refractive index modulation or thickness as a result of gas adsorption) of different sensor designs was carried out using Raman-Nath theory and Kogelnik’s Coupled Wave Theory. The influence of a range of parameters on the sensitivity of holographically-recorded surface and volume photonic structures has been studied, namely hologram geometry, hologram thickness and spatial frequency, reconstruction wavelength, and zeolite nanoparticle refractive index. From this, the optimum fabrication …

Development Of A Photopolymer Holographic Lens For Collimation Of Light From A Green Light-Emitting Diode, Sanjay Keshri, Kevin Murphy, Vincent Toal, Izabela Naydenova, Suzanne Martin

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A holographic optical element (HOE) was developed to collimate a monochromatic light-emitting diode (LED). The fabrication was achieved by the interference of collimated and diverging beams from a 532 nm laser to produce the required photonic structure in a self-developing photopolymer material. The experimental values of diffraction efficiency and spatial period across the HOE were compared with their expected theoretical values. Good agreement was found for the spatial period; however, the diffraction efficiency varied significantly across the lens. In this paper, two approaches have been taken to address this variation: (1) modification of recording geometry and (2) optimization of recording …

Enabling Quantification Of Protein Concentration In Human Serum Biopsies Using Attenuated Total Reflectance – Fourier Transform Infrared (Atr-Ftir) Spectroscopy, Kate Spalding, Franck Bonnier, Clément Bruno, Hélène Blasco, Ruth E. Board, Isabelle Benz-De-Bretagne, Hugh Byrne, Holly J. Butler, Igor Chourpa, Pretheepan Radhakrishnan, Matthew J. Baker

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Changes in protein concentrations within human blood are used as an indicator for nutritional state, hydration and underlying illnesses. They are often measured at regular clinical appointments and the current analytical process can result in long waiting times for results and the need for return patient visits. Attenuated total reflectance – Fourier transform infrared (ATR-FTIR) spectroscopy has the ability to detect minor molecular differences, qualitatively and quantitatively, in biofluid samples, without extensive sample preparation. ATR-FTIR can return an analytical measurement almost instantaneously and therefore could be deemed as an ideal technique for monitoring molecular alterations in blood within the clinic. …

Whispering Gallery Mode Micro Resonators For Multi-Parameter Applications, Arun Mallik, Gerald Farrell, Manjusha Ramakrishnan, Vishnu Kavungal, Dejun Liu, Qiang Wu Prof.

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A novel fiber optic sensing configuration for simultaneously measuring ammonia vapor (NH3) concentration and relative humidity (RH) in air is proposed and experimentally demonstrated. The system comprised two silica whispering gallery mode (WGM) microsphere resonators coated with different polymer layers. One of the microspheres was dip-coated with sol gel silica polymer and another with a 0.5 % wt./vol. agarose hydrogel. WGMs in both microspheres were excited simultaneously by evanescent coupling using a single adiabatic fiber taper. The optical properties of both coating layers change due to their exposure to ammonia and water molecules in the surrounding atmosphere, resulting in the …

Structure-Property Relationships For A Series Of Ruthenium(Ii) Polypyridyl Complexes Elucidated Through Raman Spectroscopy, Luke O'Neill, Laura Perdisatt, Christine O'Connor

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A series of ruthenium polypyridyl complexes were studied using Raman spectroscopy supported by UV/Vis absorption, luminescence spectroscopy, and luminescence lifetime determination by time-correlated single photon counting (TCSPC). -e complexes were characterised to determine the influence of the variation of the conjugation across the main polypyridyl ligand. -e systematic and sequential variation of the main polypyridyl ligand, 2-(4-formylphenyl)imidazo[4,5-f][1,10]phenanthroline (FPIP), 2-(4-cyanophenyl)imidazo[4,5-f][1,10]phenanthroline (CPIP), 2-(4-bromophenyl)imidazo[4,5-f][1,10]phenanthroline (BPIP), and 2-(4-nitrophenyl)imidazo[4,5-f][1,10]phenanthroline (NPIP) ligands, allowed the monitoring of very small changes in the ligands electronic nature. Complexes containing a systematic variation of the position (para, meta, and ortho) of the nitrile terminal group on the ligand (the para …