bluuebunny/crossref_metadata_2025 huggingface dataset:
Detection of a Single Drug Exposure in Hair
Authors: Kintz Pascal
Published: January 2023

The influence of drug incorporation on melanin affinity, lipophilicity and membrane permeability is of paramount importance. Despite their high lipophilicity levels, some drugs have quite low incorporation rates into hair, suggesting that the higher incorporation rates of basic drugs (cocaine, amphetamines, etc.) than neutral (steroids, benzodiazepines, cannabinoids, etc.) or acidic drugs are strongly related to the ability of the drug to penetrate the membrane based on the pH gradient between the blood and the acidic hair matrix. When using hair analysis as a matrix during investigative analysis (e.g. in workplace drug testing, doping, driving under the influence and drug-facilitated crime), it is important to know whether the analytical procedure is sensitive enough to identify traces of drugs or even single exposures. The concept of minimal detectable concentration in hair is of interest in order to document negative findings, but limited data are currently available in the scientific literature. Until laboratories have sensitive enough methodologies to detect a single use of a drug, care should be taken when comparing urine and hair findings.
The Usefulness of Metabolic Ratios in the Interpretation of Steroid Misuse
Authors: Brailsford A. D.
Published: January 2023

This chapter discusses the approaches used to determine testosterone (T) administration, with a particular focus on the use of metabolic ratios to facilitate the distinction between cases of T administration and naturally derived steroid profiles. Given the association of T misuse with elite sports, a brief history of this area is provided, and the approaches used to detect T administration are mainly discussed in this context. The key areas included are the use of the steroid ratios (T/epitestosterone), steroid/glycoprotein ratios (T/luteinising hormone), the athlete biological passport (longitudinal profiling of a specific athlete’s steroid profile) and the use of the carbon isotope ratio to distinguish exogenous and endogenous T. While the desire to detect T administration is sport has driven much of the research in this area, it should be remembered that T misuse and, more widely, steroid abuse is an increasing problem in society.
Genomics and Diagnostics in Acute Myeloid Leukaemia
Authors: Al Seraihi Ahad F. , Rio-Machin Ana , Tawana Kiran , Charrot Sarah , Di Bella Doriana , Bödör Csaba , Butler Tom , Farren Timothy , Grantham Marianne , Fitzgibbon Jude
Published: January 2023

Cancers can be best described as genetic diseases, where mutations typically accumulate over a protracted period of time, leading to a cellular shift from normalcy to malignancy and an ever-evolving tumour and its microenvironment. The tools at our disposal to characterise the genetic landscape(s) of these tumours and our appreciation of their complexity have fundamentally changed over the last 10 years, following the first whole-genome sequencing (WGS) of a case of acute myeloid leukaemia (AML) in 2008 and the introduction of global initiatives (e.g. The Cancer Genome Atlas (TCGA)), both with an overarching goal of improving diagnosis, treatment and cancer prevention by setting out to systematically explore the entire spectrum of genomic changes involved in human disease. While this journey is far from complete, modern diagnosis of cancers now relies on the integration of morphological and molecular information that, together, offer the potential to refine classification, establish prognosis and determine the most appropriate treatment for groups of patients. In this chapter, we examine how genomics has revolutionised our understanding of the diagnosis of blood cancers, using the exemplar of AML, and how this new knowledge is set to inform and direct treatment in the near future.
Molecular Diagnostics
Authors: Al-Turkmani M. Rabie , Tsongalis Gregory J.
Published: January 2023

This chapter focuses on advances in technologies that have led to a better understanding of the molecular basis of infectious, genetic and oncological diseases. Highly complex technologies, such as microarrays and next-generation sequencing, have resulted in biomarker discoveries that have led to the development of novel therapies and companion diagnostics. Qualitative and quantitative molecular testing continues to be critical in the management of patients with infectious disease, genetic disease and cancer. Drug development strategies that incorporate genomics have required clinical laboratories to be prepared for and routinely test for pharmacogenomic markers that address metabolic and targeted aspects of drug delivery. Clearly, the transition to high-complexity and high-data-throughput technologies will once again revolutionize how we approach diagnostic medicine with respect to patient care.
Nanomaterials in Human Disease Diagnosis
Authors: Singh Ragini , Singh Sanjay
Published: January 2023

Nanotechnology can be defined as the manipulation of matter on a molecular, atomic or supramolecular scale to control its size at the nanometer scale (1–100 nm), which leads to the origin of unique properties. Recent developments in this field have explored these unique physical, chemical and biological properties and created a new way to use nanomaterials (NMs) in various biomedical applications, particularly in treatment and diagnosis of diseases, implants, prostheses and drug delivery. In this chapter, recent advances in nanotechnology-based nano-tools for disease diagnosis and their potential application in early disease detection with high sensitivity and specificity are discussed. Vast applications of NMs in disease diagnosis have been described for some common diseases, like cancer, diabetes and other infectious diseases.
Molecular Biomarkers: Overview, Technologies and Strategies
Authors: Verma Mukesh , Barh Debmalya , Azevedo Vasco
Published: January 2023

Biomarkers play major roles in biomedicine. With the advancement of technologies and knowledge about the molecular mechanisms of disease initiation, development, and progression, biomarkers have been defined differently. For all practical purposes we have defined biomarkers as indicators of the biological state at specific time which can be measured and evaluated as indicators of biological processes, pathogenic states, pharmacological responses and therapeutic and intervention processes. We have selected few diseases (immune diseases, cardiovascular diseases, metabolomic diseases, infectious diseases, neurological diseases and cancer) to emphasize the significance of biomarkers in disease diagnosis and therapeutics. Omics technology (genomics, epigenomics, proteomics, metabolomics, transcriptomics etc.)-based potential biomarkers for better risk assessment, diagnosis, treatment and patient care (survival) are described. The significances of non-invasive biomarkers over invasive biomarkers and the potential of biomarkers in personalized medicine and genomics are also discussed. Due to the large amount of data, we have divided the contents into two chapters. In this first section we have given an overview of molecular biomarkers followed by types, discovery techniques and markers derived by such techniques for the selected diseases. In the next chapter we will discuss the challenges in biomarker discovery and the clinical implications of omics-based next-generation biomarkers. We believe that this chapter and the one that follows will be helpful to students and clinicians, as well as persons interested in cancer biomarkers.
Basic Molecular Biology Techniques
Authors: Rapley Ralph
Published: January 2023

Analysis at the molecular level is the cornerstone of modern biosciences and the utility of new and powerful ways of isolating, analysing, manipulating and exploiting nucleic acids is now essential. In recent years there has been much focus on ‘omics’ technology in a number of fields such as ‘genomics’, ‘proteomics’ and ‘transcriptomics’, among many others. This developing area attempts to address critical biological problems as a whole and the interactions within the area. This chapter details current molecular biology techniques and is intended to provide an overview of the general features of nucleic acid structure and function and to describe some of the basic methods used in their isolation and analysis. The techniques developed and employed in the manipulation of nucleic acids are essential for the analysis of cells and tissues and interactions at the molecular level.
Genes and Genomes
Authors: Whitehouse David B.
Published: January 2023

The completion of the Human Genome Project and the development of new recombinant DNA methods have paved the way for dramatic progress in many areas of molecular biology and biotechnology. They have led to advances in molecular cloning, genome-wide mapping and mutation and polymorphism detection. Indeed, the development of these methods has also led to numerous genome projects while at the same time contributing to the development of bioinformatics for the analysis of genomes from many species both in health and disease. This rapid advance and automation of some of the enabling molecular methodologies and their applications are addressed in this chapter, which identifies the key processes in the understanding of genes and genomes.
Human and Animal Cell Culture
Authors: Davis John
Published: January 2023

The culture of both human and animal cells in vitro is becoming ever more important, not only in research into the understanding, prevention and treatment of human and animal diseases, but also in the manufacture of related products such as vaccines and drugs. This chapter lays out the principles that should be used in the culture of all such cells in order to achieve meaningful and reproducible results and gives guidance on the practical implementation of these principles.
Genome Editing
Authors: Stotz Henrik U. , Koizuka Nobuya
Published: January 2023

Genome editing has perhaps become the most popular toolbox for generating targeted mutations. Over 0.3% of all publications in PubMed are currently concerned with this topic, demonstrating its importance. Since 2012, there has been an exponential explosion in research articles, owing primarily due to the clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated system (Cas). This chapter provides background understanding of the three major genome editing techniques, i.e. zinc finger nucleases, transcription activator-like effector nucleases and CRISPR/Cas. Genome editing has been applied to organisms from all three domains of life, i.e. prokaryotes, archaea and eukaryotes. This has provided powerful tools for custom engineering genes of interest, providing unprecedented possibilities for synthetic biological applications. As an example of biotechnological applications, CRISPR/Cas9 editing of crop plants is discussed. Chances and risks of genome editing are also considered, reflecting the debate among scientists and policy makers. In particular, human genome editing is of global concern and raises important ethical and regulatory issues.
Modelling and Simulation of Proteins
Authors: Patel Hershna , Kukol Andreas
Published: January 2023

Proteins are biopolymers with a complex structure and flexibility, both of which are intrinsically linked with the important functions that proteins carry out in organisms and in biotechnology applications. The first part of this chapter explains the main template-based and template-free methods of protein structure prediction, namely comparative modelling, threading/fold recognition, ab initio modelling and contact-based modelling. The second part explains the method of molecular dynamics simulation of proteins, which is used to simulate protein flexibility. In addition to standard procedures, basic data analysis and limitations are discussed. Techniques to overcome some of the limitations, such as polarisable force fields and enhanced sampling techniques, are summarised. This chapter enables readers to understand the research literature in this area and to move forward to more practical tutorials and apply the methods themselves.
Intellectual Property and Biotechnology Patents
Authors: Harbron Stuart
Published: January 2023

The formalities of the patenting process are discussed in relation to an overview of the patent landscape. Patent battles between the two main intellectual property holders, Broad Institute and the University of California, to gain dominance in this field are described in relation to the processing of patent applications at the United States Patent and Trademark Office (USPTO) and the European Patent Office (EPO). The involvement and contributions of other patentees (University of Vilnius, Toolgen and MilliporeSigma) are noted. Finally, problems of licensing are highlighted.
The Phage Nanoparticle Toolkit
Authors: Smith George P.
Published: January 2023

This chapter will review the physical and biological properties of filamentous phage that have made them a flexible platform for development of new nanoparticles. The long, thin virion is extraordinarily robust, being tolerant of harsh physical conditions, extensive chemical modification, and genetic fusion of foreign “guest” peptides and proteins to its exposed coat proteins. As much as twenty percent of its outer surface can be modified without impairing phage assembly or infectivity. Virions can be reliably produced in great abundance and purified to a high degree of purity by simple, scalable processes. Most importantly, their ability to replicate has opened up invention strategies that depend on selecting particles with desired properties from vast populations with random variations, rather than on rational design. Growing knowledge of the unusual infection cycle, along with more than three decades of experience in manipulating filamentous phages for biotechnological ends, have resulted in an extensive “toolkit” of useful, broadly applicable techniques for enhancing a new initiative's chance of success.
The Roles of Structure, Dynamics and Assembly in the Display of Peptides on Filamentous Bacteriophage
Authors: Opella Stanley J.
Published: January 2023

The filamentous bacteriophages are extraordinarily interesting biological organisms in their own right with a fascinating lifecycle that involves the host cell membrane even though they do not possess a membrane themselves. With the ability to accept additional nucleotides they have proven to be among the most useful tools in experimental molecular biology and biotechnology. The structures of the coat proteins of both Class I (fd) and Class II (Pf1) bacteriophages in both their membrane-bound and structural forms in the bacteriophage particles demonstrate fundamental complexity in the structure and dynamics of apparently small helical proteins. The structures or the end points enable a model of the assembly process to be developed. And all of this structural information informs the design and expression of peptides displayed on the surface of bacteriophages, which is one of the principal applications of these systems in biomedical and biotechnological research.
Quantitative Analysis of Peptide Libraries
Authors: Makowski Lee
Published: January 2023

Quantitative analysis of peptide libraries can provide substantial information about molecular interactions that cannot be readily extracted from a qualitative inspection of the results of a phage display experiment. Affinity screening of phage-displayed combinatorial peptide libraries is carried out in order to identify a peptide sequence or sequence motif that binds tightly to a particular molecular target. The result of the experiment is a population of phage particles that represent a subset of the original library that has been enriched for binding to the molecular target. The nucleic acid sequences of the inserts in these phage particles are used to determine the sequences of the displayed peptides whose binding properties presumably led to their selection. In some cases, a sequence motif common to some (or many) of the derived sequences is immediately apparent from a visual inspection of the selected sequences. Frequently, no readily discernable motif can be identified from a visual inspection. This does not necessarily mean that the experiment failed. There are numerous examples in which weak motifs have been identified only after detailed computational analysis of the sequences.

Quantitative analysis can provide insight into at least five aspects of phage-display technology: the quality of a peptide library; the quality or effectiveness of an affinity screen; identification of sequence motifs; identification of binding sites on a protein; and, possibly, identification of proteins that bind to a particular target within an entire genome. This Chapter reviews the existing computational methods available for analyzing populations of peptides and identification of motifs within those populations.
Phage-mediated Drug Delivery
Authors: Petrenko Valery A. , Jayanna Prashanth K.
Published: January 2023

The creation and maintenance of a drug's therapeutic concentration at its site of action has presented a pharmacological dilemma for decades. Circumventing this problem involves either creating drugs that are more target-specific or modifying existing drugs so as to result in preferential localization in target tissue. Drug delivery systems are characterized by both the drug carrier and the targeting moiety. Antibodies have been, so far, the mainstay of targeting ligands. However, problems associated with their use has allowed the emergence of peptides as a new generation of ligands. Further, the availability of phage display libraries permit high throughput selection of target-specific peptide ligands. Apart from being a source of targeting ligands, phage itself serves as an excellent vehicle for drugs. This chapter provides examples of the use of phage particles and phage components as mediators of drug targeting. Also, details of an approach in which the target-specific phage major coat protein is utilized as a liposomal ligand will be discussed in depth.
Imaging with Bacteriophage-derived Probes
Authors: Deutscher Susan L. , Kelly Kimberly A.
Published: January 2023

Filamentous bacteriophages (phages) are versatile particles useful as a platform for the development and application of molecularly targeted in vivo imaging agents. They can not only be genetically modified for the generation of diverse phage display libraries suitable for selection of specifically targeted antibodies, peptides, and proteins; they can also be chemically modified for use in the field of molecular imaging, nanomedicine, nanodevices, biosensors, and gene transfer. Phages are among the most promising new type of biological nanomaterial in that they represent ideal monodisperse nanoparticles that are able to self-assemble, are biodegradable, and non-pathogenic.
Phage-based Pathogen Biosensors
Authors: Li Suiqiong , Lakshmanan Ramji S. , Petrenko Valery A. , Chin Bryan A.
Published: January 2023

The phage engineering, which grounds on the natural mechanisms of selection, allows directed nanofabrication of bioselective materials, with possible applications to biosensors, nanoelectronics, biosorbents, and other areas of medicine, technology, and environmental monitoring. In particular, using phage display technology allows the generation of libraries possessing diverse nanostructures accommodated on the phage's surface – a huge resource of diagnostic and detection probes. Selected phage-derived probes bind biological agents and generate detectable signals as a part of analytical platforms. They may be suitable as robust and inexpensive molecular recognition interfaces for field-use detectors and real time monitoring devices for biological and chemical threat agents. The data discussed in this chapter shows how the use of phage-based interfaces may greatly improve the sensitivity, robustness and longevity of commercial biosensors.
Genetically Engineered Virulent Phage Banks for the Detection and Control of Bacterial Biosecurity Threats
Authors: Iris François , Pouillot Flavie , Blois Hélène , Gea Manuel , Lampe Paul-Henri
Published: January 2023

Natural outbreaks of multidrug-resistant microorganisms can cause widespread devastation, and several can be utilized or engineered as agents of bio-terrorism (emergent strains). From a bio-security standpoint, the capacity to detect and then efficiently control, within hours, the spread and the potential pathological effects of an emergent outbreak, without recourse to either antibiotics or vaccines, become key challenges that must be met. We turned to phage engineering as a potentially highly flexible and effective means to both detect and eradicate threats originating from emergent (uncharacterized) bacterial strains. To this effect, we developed technologies allowing us to 1) concurrently modify multiple regions within the coding sequence of a gene while conserving intact the remainder of the gene, 2) reversibly interrupt the lytic cycle of an obligate virulent phage (T4) within its host, 3) carry out efficient insertion, by homologous recombination, of any number of engineered genes into the deactivated genomes of a T4 wild-type phage population and 4) reactivate the lytic cycle, leading to the production of engineered infective virulent recombinant progeny. This allows the production of very large, genetically engineered lytic phage banks containing, in an E. coli host, a very wide spectrum of variants for any chosen phage-associated function, including host-range. Rapid screening of such a bank allowed the isolation of recombinant T4 particles capable of detecting (diagnosis), infecting and destroying hosts belonging to gram-negative bacterial species evolutionarily close (Yersinia ruckeri) as well as far removed (Pseudomonas aeruginosa) from the original E.coli host (DK8).
Phage Vaccines and Phage Therapy
Authors: Manoutcharian Karen
Published: January 2023

The application of combinatorial approaches in conjunction with phage display techniques might be critical for development of vaccines against various infective and cancer diseases. Phage technique allows the generation of novel immunogens representing structural/molecular mimics of pathogen-derived immunodominant epitopes, or protein domains displayed on phages capable of inducing protective antibodies, or construction of novel vaccines based on incorporation of antigenic/genetic variability of pathogens or cancer cells in the context of phage particles. The diversity of applications and success of phage display are due to its simplicity and flexibility along with the possibilities of very cheap large-scale production of phage particles by recovering them from infected bacterial culture supernatants as nearly 100% homogenous preparations. Phages are easy to manage, they resist heat and many organic solvents, chemicals, or other stresses, and, importantly, phage particles are highly immunogenic and do not require adjuvant. Furthermore, phages do not require the cold chain (requirement to store vaccines at refrigerated or frozen temperatures), which equates to lower transport and storage costs. Considering these points, recombinant phages should be viewed as promising vaccine discovery tools and vaccine delivery vectors, and it is worth even considering the possibility of replacing the delivery systems of known vaccines currently in use with phage particles as vaccine carriers. The chapter outlines the current advances in phage vaccine development and analyses possible advances of phages as engineered immunogens.
Actions of Drugs on the Cardiovascular and Renal System
Authors: Blackburn Thomas P.
Published: January 2023

This chapter presents the physiological/pharmacological properties and therapeutic uses of drugs acting on the cardiovascular and renal system (CRS). The basic principles of pharmacology and development from physiology, medicinal chemistry to an increasing, sometimes vague understanding of the pathophysiology and the disease state are highlighted. Pharmacology is just one stanza in our understanding of drug action on organ systems in the body.
The Future of ADME in Drug Design and Development
Authors: Jeffrey Phil , Summerfield Scott
Published: January 2023

ADME (absorption, distribution, metabolism and excretion) are the descriptive terms applied to the multiple and complex processes that govern drug distribution. DMPK (drug metabolism and pharmacokinetics) is the scientific discipline that has evolved to provide the qualitative and quantitative study of these processes throughout the drug discovery and development lifecycle and, as such, is very much a cradle to grave discipline. Successful drug discovery and development requires an integrated clinical focus from the outset. Once a compound enters drug development it cannot be re-engineered or modified. It therefore falls to the Medicinal Chemist, with one eye steadfastly fixed on the clinical prize, to design, select and progress only those compounds that have the correct biological profile and physicochemical properties for clinical evaluation. Fulfilling a critical role in supporting the selection of potent, selective leads that retain the appropriate physicochemical properties to ensure distribution from the site of administration to the site action, DMPK bridges the gap between the disciplines of biology and chemistry, thereby enabling and maintaining a clinical focus in the early discovery phase. Accordingly, a fundamental understanding of this scientific discipline is essential for any Medicinal Chemist working in the field of drug discovery. DMPK is, by necessity, a broad and multifaceted science and a wide variety of in vitro and in vivo assays are used to triage and select compounds for progression. However, no one assay has the power to improve all the odds for overall success and therefore data integration and contextualisation are now emerging as key areas of growth and scientific development. This chapter highlights the pivotal role of ADME in early drug discovery including basic principles, the consideration of “free” drug concentrations with respect to drug absorption, drug–drug interactions and concentrations at the target site of action. The evolving sciences of early and earlier human pharmacokinetic predictions aligned with estimates of clinical therapeutic dose are introduced and the concept of a more systems-based approach is advocated.
Predicting Dose and Selective Efficacy in Clinical Studies from Preclinical Experiments: Practical Pharmacodynamics
Authors: Hill R. G.
Published: January 2023

Animal pharmacology experiments to establish putative efficacy and to predict dose in subsequent human subject investigations have been, and continue to be, an important part of the drug discovery process. The predictive value of such animal work is sometimes minimal and this chapter reviews the reasons for this and suggests ways in which the most robust data can be obtained. The use of chiral molecules to obtain data that is reliably associated with the pharmacological target and the use of surrogate endpoints are considered. The problem of species differences in pharmacology is dealt with in the context of neuropharmacological studies of the role of substance P. The importance of imaging studies and ways in which reproducibility can be improved are also briefly considered.
Introduction
Authors: Barton Steve , Eastham Allan , Isom Amanda , Mclaverty Denise , Soong Yi Ling , Polowyj Rachael
Published: January 2023

Reading this book, you will discover that, while cosmetic products often sit on the surface, they are not as superficial as often thought. In this introductory chapter, we have tried to prepare you for the scientific terms and concepts you will come across in the subsequent chapters, which will be explained in more detail as they arise in the text.
You Against the World! – The Science Behind Skin and Skincare Products
Authors: Parker Robin , Roberts Nichola , Burke Monique
Published: January 2023

In order to understand the science of skin care, it's important that the cosmetic scientist has a basic understanding of skin itself. In this chapter we look at the structure of skin and find out how it works and the best ways to maintain healthy-looking skin. The process of ageing is explored and why our skin goes through the changes it does through a lifetime. The role played by the microbiological community that lives on and in human skin is also discussed, along with ways skincare products can potentially influence this important symbiotic relationship. We move on to the skincare products themselves and discuss how they work to improve the appearance of skin and consider the best ways of achieving effective moisturization. The practicalities of how to make a cosmetic emulsion product stable by choosing the correct emulsifier blend and how to make if feel amazing when applied to the skin are all discussed. Finally, we look at the different types of skincare available, why skincare regimes work and why we need different products for different parts of the body.
Glass, Ceramics and Enamelled Objects
Authors: Colomban P.
Published: January 2023

Much like weapons, vessels made from glasses and ceramics have long been held as objects of very high technology. Ceramic technology mastery is even at the foundation of metallurgy. In producing glass, pottery and enamelled metals, three critical and energy intensive steps are needed: obtaining fine powder, firing, and building appropriate kilns. Control of the colour also requires advanced physical and chemical knowledge. Indeed, if ceramic production is somewhat the art of forming a heterogeneous matter (only some components melt), glass or enamel production requires the object to pass through a homogeneous liquid state to obtain the desired microstructure and properties. This chapter presents the different destructive, non-destructive and non-invasive analytical methods that can be carried out in a laboratory on shards or sampling with fixed ‘big’ instruments, or on-site (museums, reserves, etc.) with mobile set-ups. After a brief overview of the history of pottery, the implications of the processes involved (grinding, shaping, sintering, enamelling, decoration) on micro- and nano-structures (formation and decomposition temperature, kinetic and phase rules, sintering) is given. Emphasis is given to information that can be obtained by XRF and Raman mobile non-invasive measurements. Examples illustrating how these studies help to document technology exchanges and exchange routes are also given.
The Need for Innovations in Higher Level Chemistry Education – A Pedagogical Justification
Authors: Byers Bill , Eilks Ingo
Published: January 2023

Higher Education is currently experiencing a period of unprecedented change. In Europe the Bologna Process is necessitating changes to the duration and structure of many courses while the Lisbon Agenda, which seeks to develop a Knowledge-Based European Economy, is identifying the need for many more graduates in key areas including chemistry. It is clear that the traditional teaching methods will be inadequate and inappropriate to support the mass higher education system that is now emerging. This book has been written as a guide for all lecturers interested in developing their chemistry teaching in order to promote more effective student learning at Universities and other higher education institutions. This first chapter introduces readers to important aspects of modern learning theory, and from this starting point goes on to provide a pedagogical justification for the need for new and innovative methods to be applied in higher level chemistry education with the aim of promoting the meaningful learning required to educate future generations of chemistry graduates. The chapter therefore aims to motivate readers to develop their own teaching using pedagogically sound strategies.
The Uniqueness of Teaching and Learning Chemistry
Authors: Floriano Michele A. , Reiners Christiane S. , Markic Silvija , Avitabile Gustavo
Published: January 2023

Unfortunately, the current perception of Chemistry held by many students and the general public alike appears to be in stark contrast to its true nature. Although chemistry is ubiquitous in all aspects of our daily lives it continues to be perceived as highly theoretical and of little relevance. A clearer understanding of the fundamental Nature of Chemistry will be needed if students are to recognize its true importance and character. It is not possible to fully understand, and as a consequence accept on an intuitive basis, the 'mystery' and fascinations arising from the transformation of matter, without first adopting a convincing sub-microscopic view, able to connect observed macroscopic properties to the behaviours of atoms and molecules. Insightful use of models and computer generated visualization techniques now offer a way forward, but only once the learning difficulties being encountered by students have been fully appreciated by their university lecturers.
Context- and Problem-based Learning in Higher Level Chemistry Education
Authors: Overton Tina L. , Byers Bill , Seery Michael K.
Published: January 2023

Context and problem-based learning are approaches to teaching that have been found to engage and motivate students and to develop a range of intellectual and transferable skills. This chapter discusses the literature related to these approaches and describes strategies to implement them in the teaching of chemistry within higher education.
Online Support and Online Assessment for Teaching and Learning Chemistry
Authors: Brouwer Natasa , McDonnell Claire
Published: January 2023

In this chapter, examples of innovative approaches that use educational technology to support active learning in chemistry lectures, tutorials and laboratory sessions are considered. The scope of the chapter is limited to blended learning. The strengths and weaknesses of e-learning are examined and the options available for online assessment using electronic tests and e-portfolios are discussed. In addition to the literature references provided in the chapter, several examples of good practice involving the implementation of information and communication technology for chemistry teaching in higher education are incorporated. A list of online resources for lecturers is also included.
Catalytic Systems for the Morita–Baylis–Hillman Reaction
Authors: Zhao Mei-Xin , Wei Yin , Shi Min
Published: January 2023

A remarkable number of effective catalysts have been identified and developed for Morita-Baylis-Hillman reaction and its asymmetric version. This Chapter will discuss achiral or chiral catalytic systems for the Morita-Baylis-Hillman reaction, which include amine-catalyzed system, phosphine-catalyzed system, Lewis acids-catalyzed system, co-catalyzed system, as well as polymer supported catalysts.
Nucleic Acids as Biorecognition Element in Biosensor Development
Authors: Erdem Arzum , Ozsoz Mehmet
Published: January 2023

Nucleic acids and their role in living organisms is described. A classification of nucleic acids, in terms of their natural or synthetic origin, is presented. The use of nucleic acids, both natural and synthetic, as bioreceptors in biosensor technology is discussed with reference to specific examples.
Aptamer-based Biosensor for Environmental Monitoring
Authors: Cella Lakshmi N. , Chen Wilfred , Mulchandani Ashok
Published: January 2023

Since their discovery, aptamers have captivated the attention of researchers. Today aptamers are available for a wide variety of target molecules ranging from metal ions to whole cells. In this chapter the description of aptamer production and of their interesting properties for biosensing are reported. Applications to environmental monitoring, such as detection of pathogens, toxins, drugs, and organic and inorganic pollutants, are also illustrated.
Nucleic Acid-based Biosensors for the Detection of DNA Damage
Authors: Rogers Kim R. , Gary Ronald K.
Published: January 2023

Determination of the extent of environmental hazards in polluted water, soil, and sediments is of tremendous importance for managing risks to human health and the environment. Toxicity screening tests allow rapid identification of the presence of potentially harmful substances in environmental matrices. One mechanism for toxicity is genotoxicity. In this chapter, the importance of the development of short-term tests for genotoxicity evaluation is demonstrated as well as the role of biosensors for DNA damage. Biosensor-based genotoxicity assays involve the measurement of chemically induced damage to surrogate DNA or the responses of genetically engineered microorganism reporters that express proteins that can be measured when these organisms are challenged by DNA-damaging chemicals. These two types of systems are described with special emphasis on optical detection.
Detection of Damage to DNA Using Electrochemical and Piezoelectric DNA-Based Biosensors
Authors: Labuda Jan
Published: January 2023

DNA is an electroactive compound and electroanalysis is considered to be a fundamental technique in studying DNA damage, detecting low levels of genotoxic substances, and studying their effects on DNA. Moreover, electroanalysis can be used to evaluate the DNA protection (antioxidative) capacity of various natural and synthetic substances. This chapter deals entirely with the use of electrochemical and piezoelectric DNA biosensors to detect, induce, and control DNA damage. The state of the art in detection principles and applications of DNA biosensors in recent years is reviewed.
Algorithms for Predicting the Physical Properties of Nanocrystals and Large Clusters
Authors: Chelikowsky James R.
Published: January 2023

The electronic structure problem for nanoscale systems is a computationally challenging problem. The large number of degrees of freedom, both electronic and nuclear, and requiring a highly precise solution, make the problem impossible to solve without some effective approximations. Here I illustrate some advances in algorithm developments by solving the electronic structure problem within density functional theory in real space using pseudopotentials and density functional theory. The algorithms presented are based on a Chebyshev-filtered subspace iteration, which results in a significant speedup over methods based on standard sparse iterative diagonalization. I illustrate this method for a variety of nanostructures by calculating the electronic and vibrational states for silicon nanocrystals, the electronic properties of doped semiconductor nanocrystals, and the magnetic properties of metallic iron clusters.
Rational Design of Mixed Nanoclusters: Metal Shells Supported and Shaped by Molecular Cores
Authors: Naumkin Fedor Y.
Published: January 2023

This work considers a variety of core–shell systems with atom to small to larger molecule inside cluster cages of a few different metals. Evolution of the system structure and some related properties are followed with changing the shell size and material, and the core–shell interaction from covalent to noncovalent, for the latter case with and without a charge transfer between the core and the shell. Different inserted “dopands” are shown to reshape the host cage slightly or considerably, and the stability of the resulting species is found to be sensitive to the specific core+shell combination (from unstable to metastable to stable). Together with a rich variation of the electronic properties (charge distributions, excitation and ionisation energies, electron affinities) upon such a ‘doping’, this can enable a flexible design of systems with desirable geometric and physical-chemical parameters for numerous potential applications. Some other specific aspects discussed include dis- and similarities of metallocarbon and hydrocarbon species, separation of the system property alterations due to change of the cage shape alone and due to further core–shell bonding, hypercoordination of the core atoms, as well as mutual influence of the core and the shell, possible shell-induced and -aligned chemical reactivity of the core.
Self-Assembly of Nanoclusters: An Energy Landscape Perspective
Authors: Chakrabarti Dwaipayan , Fejer Szilard N. , Wales David J.
Published: January 2023

Judicious design of building blocks is the key to nanofabrication via programmed self-assembly. This overview highlights how a survey of the underlying potential energy surface can provide valuable insight into designing building blocks for efficient self-assembly. Illustrative examples are considered within a recently developed computational framework for geometry optimisation of rigid bodies.
Computational Electrodynamics Methods
Authors: Harris Nadine , Ausman Logan K. , McMahon Jeffrey M. , Masiello David J. , Schatz George C.
Published: January 2023

This chapter has focused on a number of commonly used analytical and numerical electrodynamics methods that can be used to model the optical properties of plasmonic nanostructures, with emphasis on nonconventional applications of these methods to problems that have been recently been of interest in the surface spectroscopy field, especially surface-enhanced Raman scattering (SERS). A dipole reradiation (DR) methodology was added to the analytical approach of Mie theory to DR effects in SERS intensities, which is a more accurate expression for the electromagnetic enhancement theory than the commonly used plane-wave (PW) enhancement expression. We show that DR/PW differences can be significant for certain choices of detector locations due to interference and multipole effects, and generally the DR enhancements are smaller than PW. The numerical 2D finite-difference time-domain (FDTD) method was modified through the incorporation of the hydrodynamic Drude model dielectric constant, enabling the calculation of spatially nonlocal dielectric responses for arbitrarily shaped nanostructures. Nonlocal effects become important when structural features extend below around 10 nm where the dielectric constant becomes a function of both the wavevector and the frequency. The importance of including nonlocal effects was demonstrated by calculating the optical response of cylindrical and triangular nanowires. The discrete dipole approximation (DDA) provides an alternative method for determining nanoparticle optical properties that uses a similar grid to FDTD, but with different convergence characteristics. We show that for cube-shaped particles the two methods have similar convergence behavior, but accuracy is a problem for DDA, while representing the frequency dependence dielectric constant is a problem for FDTD. A general many-body formalism describing plasmon-enhanced linear spectroscopies was developed by linking the numerical DDA method with electronic structure theory based on Q-Chem. This methodology allows the calculation of the linear-response and scattering properties between a molecule, which is described quantum mechanically, interacting with a classically described metal nanostructure. To demonstrate this formalism the linear response and scattering of a pyridine–Ag spheroidal system was calculated as a function of excitation energy and aspect ratio.
Computational Study of the Formation of Inorganic Nanotubes
Authors: Wilson Mark
Published: January 2023

Computational investigations of the structures of inorganic nanotubes (INTs) are described. Discussions are restricted to two classes of INT found to form in the MX stoichiometry and whose structures can be rationalised by reference to the folding of two classes of two-dimensional net. Modelling methodologies, to investigate the formation and stability of these structures, are introduced and utilised. The energetics of the resulting INTs are discussed in terms of the underlying interatomic interactions. The use of dynamic simulation methods allows the primary mechanisms of formation to be identified. The formation of INTs is discussed by reference to their underlying energy landscapes.
Native and Irradiation-Induced Defects in Graphene: What Can We Learn from Atomistic Simulations?
Authors: Kotakoski Jani , Krasheninnikov Arkady V.
Published: January 2023

Defects in graphene, a recently discovered one-atom-thick material with exceptional characteristics, may considerably alter its properties and have negative effects on the operation of graphene-based electronic devices. Defects, when deliberately created by ion and especially electron irradiation with a high spatial resolution, may also have a beneficial effect on the target. Thus the complete understanding of the energetics and dynamics of defects in graphene is required for engineering the properties of graphene-based materials and devices. In this Chapter we give an overview of the recent progress in the understanding of the role of defects in these materials. We briefly dwell on the experimental data on native and irradiation-induced defects in graphene, and give detailed account of recent simulation results for point and line defects in graphene. We also discussed at length the mechanisms of defect formation under ion and electron irradiation as revealed by atomistic computer simulations.
The Atomic-, Nano-, and Mesoscale Origins of Graphite's Response to Energetic Particles
Authors: Heggie Malcolm I. , Latham Christopher D.
Published: January 2023

A rich variety of phenomena are observed when graphite is exposed to high doses of radiation from energetic particles. Most notably, the crystals expand along their c-axes, and dimension changes of tens of percent or even more are easily achieved. There are significant changes to the thermal and electrical properties of the material as well. When irradiation occurs below about 400 K, energy accumulates in the material, and the amount can be large in proportion to the specific heat. Known as Wigner energy, this is released by annealing, and is accompanied by a partial reversal of the initial changes, including conservation of the crystal volume. Nevertheless, the original dimensions of the crystals are not restored. The origins of this behaviour are spread over the atomic, nanometre, and mesoscale. They lie in the generation of Frenkel pairs and, we argue, dislocations. Models based on density functional theory provide insight into the likely nature and evolution of the defect structure during and after radiation.
Synergistic effects in the activation of small molecules by s-block elements
Authors: O’Hara Charles T.
Published: January 2023

This critical review covers recent developments in the special chemistry which can take place when two different s-block metals are combined within the same organometallic mixture or reagent. It will cover a selection of the most widely researched mixed-metal ‘synergic’ systems, and will be confined to mixed alkali metal/magnesium reagents. An overview of the known structural chemistry of these fascinating systems will be presented along with some of their pertinent, recent uses in synthesis, including, in the activation/cleavage of C-H bonds (i.e., a metallation reaction) or induction of metal-halogen exchange in organic molecules. The chapter begins by providing a brief historical overview of mixed s-block metal chemistry.