Academic literature on the topic 'Organic Chemistry not elsewhere classified'

Neuroendocrine tumors (NETs) throughout the body are the focus of much current interest. Most occur in the gastrointestinal tract and have shown a major increase in incidence over the past 30 years, roughly paralleling the world-wide increase in the use of proton pump inhibitor (PPI) drugs. The greatest rise has occurred in gastric carcinoids (g-NETs) arising from enterochromaffin-like (ECL) cells. These tumors are long known to occur in auto-immune chronic atrophic gastritis (CAG) and Zollinger-Ellison syndrome (ZES), with or without multiple endocrine neoplasia type-1 (MEN-1), but the incidences of these conditions do not appear to have increased over the same time period. Common to these disease states is persistent hypergastrinemia, generally accepted as causing g-NETs in CAG and ZES, and postulated as having similar tumorigenic effects in PPI users. In efforts to study the increase in their occurrence, g-NETs have been classified in a number of discussed ways into different grades that differ in their incidence and apparent pathogenesis. Based on a large amount of experimental data, tumorigenesis is mediated by gastrin’s effects on the CCK2R-receptor on ECL-cells that in turn leads to hyperplasia, dysplasia, and finally neoplasia. However, in all three conditions, the extent of response of ECL-cells to gastrin is modified by a number of genetic influences and other underlying risk factors, and by the duration of exposure to the hormonal influence. Data relating to trophic effects of hypergastrinemia due to PPI use in humans are reviewed and, in an attached Appendix A, all 11 reports of g-NETs that occurred in long-term PPI users in the absence of CAG or ZES are summarized. Mention of additional suspected cases reported elsewhere are also listed. Furthermore, the risk in humans may be affected by the presence of underlying conditions or genetic factors, including their PPI-metabolizer phenotype, with slow metabolizers likely at increased risk. Other problems in estimating the true incidence of g-NETs are discussed, relating to non-reporting of small tumors and failure of the Surveillance, Epidemiology, and End Results Program (SEER) and other databases, to capture small tumors or those not accorded a T1 rating. Overall, it appears likely that the true incidence of g-NETs may be seriously underestimated: the possibility that hypergastrinemia also affects tumorigenesis in additional gastrointestinal sites or in tumors in other organ systems is briefly examined. Overall, the risk of developing a g-NET appears greatest in patients who are more than 10 years on drug and on higher doses: those affected by chronic H. pylori gastritis and/or consequent gastric atrophy may also be at increased risk. While the overall risk of g-NETs induced by PPI therapy is undoubtedly low, it is real: this necessitates caution in using PPI therapy for long periods of time, particularly when initiated in young subjects.

Fastigiatine, C19H28N2O, is a minor component of the alkaloids of Lycopodiumfastigiatum R•Br•collected in New Zealand. Its structure and relative configuration have been resolved by an X-ray analysis of the free base. The pentacyclic ring system of fastigiatine has not been previously observed in the Lycopodium family of alkaloids or elsewhere. A proposal is presented for its derivation from the tetracyclic flabellidane ring system that is widely distributed among Lycopodium species. The mass spectrum and the 13C and 1H nmr spectra of fastigiatine are discussed.

Organic chemistry is possibly the most visual science of all chemistry disciplines. The process of scientific inquiry in organic chemistry relies on external representations, such as Lewis structures, mechanisms, and electron arrows. Information about chemical properties or driving forces of mechanistic steps is not available through direct perception, and thus looking beyond the respresentation is challenging for learners. In this study, we investigated the categorization behavior of undergraduate students enrolled in an organic chemistry course when engaged in various categorization tasks involving electrophilic addition reactions to alkenes. The critical attribute a student chose to make a category out of a set of reactions was classified as perceptual or relational and gave insights into how students process and store information about reactions at an early level of expertise. Our results support the notion that students are prone to the surface level of representations and make sense of reactions depicted in a very minimalistic fashion. Implications for approaching this phenomenon in teaching are discussed.

The metazoan meiobenthos was investigated in an Antarctic coastal sediment (Factory Cove, Signy Island, Antarctica). The fine sands contained much higher abundances compared to major sublittoral sediments worldwide. Classified second after Narrangansett Bay (North Atlantic) they reached numbers of 13 × 106ind m-2. The meiofauna was highly abundant in the surface layers, but densities decreased sharply below 2 cm. Vertical profiles mirrored steep gradients of microbiota, chloropigments and organic matter and were coincident with chemical stratification. Spatial patchiness manifested especially in the surface layer. Nematodes dominated (up to 90%), andAponema, Chromctdorita, Diplolaimella, Daptonema, MicrolaimusandNeochromadoraconstituted almost the entire community. Overall, the nematode fauna showed a strong similarity with fine sand communities elsewhere. The dominant trophic strategies were epistrarum and non-selective deposit feeding, but the applied classification for feeding guild structure of the nematodes of Factory Cove is discussed. High standing stock, low diversity and shallow depth distribution may have occurred because of the high nutritive (chlorophyll exceeded lOOOmgm-2and constituted almost 50% of the organic pool) and reductive character of the benthic environment. These observations must have originated from the substantial input of fresh organic matter from phytoplankton and microphytobenthic production, typical for an Antarctic coastal ecosystem during the austral summer.

In this review, two sort of materials i.e layered and porous materias which were studied by the author and coworkers intensively and extensively will be described. These materials generally can be classified into two groups, namely layered organic and inorganic materials and porous organic and inorganic materials. To the materials which classified in the first group, it will be discussed the syntheses, characterization and application of layered organic materials of imidazolium-dimesylamidate and of layered inorganic materials of montmorillonite. For the second group, as examples we will analogically describe the syntheses, characterization and application of 2,6-dimethylpyridinium-di(methanesulfonyl)amidate porous organic material and zeolite and pillared clay porous inorganic materials. Keywords: layered materials, porous materials, syntheses, characterization, application.

5-Hydroxymethylfurfural (HMF) is a very promising component for bio-based plastics. Efficient synthesis of HMF from biomass is still challenging because of fast degradation of HMF to by-products under formation conditions. Therefore, different studies, conducted mainly in monophasic and biphasic batch systems with and without water addition have been published and are still under investigation. However, to produce HMF at a large scale, a continuous process is preferable. Until now, only a few studies have been published in this context. In this work, it is shown that fluorous alcohol hexafluoroisopropanol (HFIP) can act as superior reaction solvent for HMF synthesis from fructose in a fixed bed reactor. Very high yields of 76% HMF can be achieved in this system under optimized conditions, whilst the catalyst is very stable over several days. Such high yields are only described elsewhere with high boiling reaction solvents like dimethylsulfoxide (DMSO), whereas HFIP with a boiling point of 58 °C is very easy to separate from HMF.

The mechanism, exciton leaking channels, and reported molecular design strategies of TADF emitters for high-performance nondoped OLEDs are summarized. Their molecular structures depending on the functional A groups are further classified.

Functionalized Tris[2-(dimethylamino) ethyl] amine (Me6TREN) ligands tethered-Fe3O4@Me6TREN nanoparticles (NPs) with a size of 150 nm were prepared to achieve classified and easy recovery of heavy metal ions in wastewater. The preparation of such NPs related to sequential silane ligand exchange and a following cure and Schiff base reactions for Fe3O4 NPs. Fe3O4@Me6TREN NPs as an effective nano-adsorbent of heavy metals exhibited significant differences in maximum adsorption capacity for Cr(III) (61.4 mg/g), Cu(II) (245.0 mg/g), Pb(II) (5.3 mg/g), and Cd(II) (1136.2 mg/g), in favor of classified removal of heavy metals from wastewater. Furthermore, Fe3O4@Me6TREN NPs can be regenerated by desorbing metal ions from NP surfaces eluted with ethylenediaminetetraacetic acid disodium salt (EDTA-Na2) aqueous, which endows such NPs promising potency as new nano-vectors for the removal of heavy metals.

Telomeres are DNA-protein complexes that cap and protect the ends of linear chromosomes. In almost all species, telomeric DNA has a G/C strand bias, and the short tandem repeats of the G-rich strand have the capacity to form into secondary structures in vitro, such as four-stranded G-quadruplexes. This has long prompted speculation that G-quadruplexes play a positive role in telomere biology, resulting in selection for G-rich tandem telomere repeats during evolution. There is some evidence that G-quadruplexes at telomeres may play a protective capping role, at least in yeast, and that they may positively affect telomere maintenance by either the enzyme telomerase or by recombination-based mechanisms. On the other hand, G-quadruplex formation in telomeric DNA, as elsewhere in the genome, can form an impediment to DNA replication and a source of genome instability. This review summarizes recent evidence for the in vivo existence of G-quadruplexes at telomeres, with a focus on human telomeres, and highlights some of the many unanswered questions regarding the location, form, and functions of these structures.

Bacteria can cause many different types of infections. Virulence factors e.g. adherence proteins, biofilm formation, endotoxins and exotoxins allow invasion by bacteria and cause infections such as respiratory, urinary, and intestinal and blood stream infections. If left untreated they can lead to a condition known as sepsis. Sepsis is a whole body inflammatory response that can be fatal. The aim of this study is to develop biomimetic nanosponges from mammalian erythrocyte ghosts, as a potential treatment for toxin related sepsis.

The design of a novel photoelectrochemical sensor, the micro-optical ring electrode (MORE), is described. Based on a thin-ring microelectrode and using at fibre-optic light guide as the insulating material interior of the ring, the MORE has been deisigned, constructed and developed to permit electrochemical investigation of photochemically generated solution species. Initial characterisation of the electrode behaviour in the dark has been ccomplished by the use of ferricyanide in conjunction with predictive mathematical models of the time dependence of the current at micro ring electrode. The photocharacterisation of the MORE has been achieved looking at the photochemical response of tris (2,2'biyridine)ruthenium(II) in presence of the quenching agent Fe3+ . Subsequent application of the MORE has been in the electrochemical investigation of photoactive drugs employed in Cancer Therapy. In the following study, the microelectrochemistry of methylene blue, a dye commonly employed on Photodynamic Therapy (PDT), has been characterised in the dark using, in the first instance, gold disc microelectrodes. The electrochemical behaviour of MB+ on gold disc microelectrodes has than been compared to the results obtained when using the MORE. Exploration of the photoelectrochemical response of the MORE is reported, achieved via the interrogation of the photoelectrochemistry of MB+. Photocurrent signals obtained during cyclic voltammetric and chronoamperometric studies of MB\ conducted with the MORE under illuminated conditions and in the absence of any deliberately added reducing agent, are attributed to the formation and subsequent detection of 3 MB+ within the diffusion layer of the microring electrode. The data demonstrate that the use of the MORE for direct electrochemical detection of photogenerated species with lifetimes of < 9 x 5 10- s is possible. The electrochemistry of 3MB+ over the applied potential range from -0.4 to +1.0 V versus SCE is elucidated and discussed in the context of the behaviour of photoexcited MB+ in the presence of deliberately added reducing agent Fe3+. In order to investigate the production of singlet oxygen associated with cancer treatment, an attempt was made to study the MB+/02 system. This part of the project has not been completed, however a preliminary study of the electrochemistry of the MB.

This dissertation describes the development of a system for the automated, high-throughput screening of organic reactions. This system utilizes a liquid handling robot for reaction mixture preparation combined with desorption electrospray ionization mass spectrometry (DESI-MS) for reaction mixture analysis. With an analysis speed of ~1 second per reaction mixture, this system is capable of screening thousands of reactions per hour. Reaction mixtures are prepared in 384-well microtiter plates using a liquid handling robot. A sample of each reaction mixture (50 nL) is then transferred to a PTFE coated, glass slide using a pin tool. By offsetting the placement of the pin tool during each transfer, up to 6,144 unique reaction mixtures can be placed on each slide. The slide is then transferred to the DESI stage by a robotic arm, and the DESI-MS analysis begins, taking as little as 7 minutes for 384 reaction mixtures. We utilize a scheduling software to control each component of the system, which automates the entire process from reaction mixture preparation to DESI-MS analysis. In order to efficiently analyze and visualize the extremely large data sets generated by the system, we developed a custom software suite to automatically process each data set. We have used this system to screen several classes of industrially relevant reactions including Suzuki coupling, nucleophilic aromatic substitution, reductive amination, and Sonogashira coupling. We have validated both positive and negative results from the system using flow chemistry, and we have observed excellent agreement between the two methodologies. By being capable of screening thousands of reactions per hour, requiring only microliter quantities of reaction mixtures, and consuming less than a milliliter of solvent during the DESI-MS analysis, this system significantly reduces the time and costs associated with organic reaction screening.

Chemical science spans multiple scales, from a single proton to the collection of proteins that make up a proteome. Throughout my graduate research career, I have developed statistical and machine learning models to better understand chemistry at these different scales, including predicting molecular properties of molecules in analytical and synthetic chemistry to integrating experiments with chemo-proteomic based machine models for drug design. Starting with the proteome, I will discuss repurposing compounds for mental health indications and visualizing the relationships between these disorders. Moving to the cellular level, I will introduce the use of the negative binomial distribution to find biomarkers collected using MS/MS and machine learning models (ML) used to select potent, non-toxic, small molecules for the treatment of castration--resistant prostate cancer (CRPC). For the protein scale, I will introduce CANDOCK, a docking method to rapidly and accurately dock small molecules, an algorithm which was used to create the ML model for CRPC. Next, I will showcase a deep learning model to determine small-molecule functional groups using FTIR and MS spectra. This will be followed by a similar approach used to identify if a small molecule will undergo a diagnostic reaction using mass spectrometry using a chemically interpretable graph-based machine learning method. Finally, I will examine chemistry at the proton level and how quantum mechanics combined with machine learning can be used to understand chemical reactions. I believe that chemical machine learning models have the potential to accelerate several aspects of drug discovery including discovery, process, and analytical chemistry.

Since 1981, HIV/AIDS has affected over 70 million individuals worldwide. Due to the incorporation of Combination Antiretroviral Therapy (cART), this deadly virus has now become a manageable chronic illness with a reduction in mortality and morbidity rates. Combination therapy targets multiple stages of the HIV replication cycle including fusion, entry, reverse transcription, integration, and maturation. The HIV-1 protease enzyme is responsible for cleavage and processing of viral polyproteins into mature enzymes and is a common therapeutic target for inhibition of HIV. To date, there have been many protease inhibitors approved by the FDA and introduced into the market. However, mutations within the protease enzyme has rendered some of these inhibitors ineffective. This has led to an ever-growing need to develop novel protease inhibitors to combat drug resistance through mutations. Described herein is the design, synthesis, and biological evaluation of HIV-1 protease inhibitors featuring a novel hexahydropyrrolofuran (HPF) bicyclic scaffold as a P₂ ligand to target binding interactions with Asp29 and Asp30. The HPF ligand provides a molecular handle that allows for further structure-activity discoveries within the enzyme. The HIV-1 protease inhibitors discussed feature carbamate, carboxamide, and sulfonamide derivatives which displayed good to excellent activity.

Organic nitrogen compounds are important in environmental systems because they are prevalent in natural waters but are also components of polymers within membrane filters that are used for water treatment. In both of these cases, these compounds can be exposed to free chlorine during disinfection, which can trigger a set of reactions that can form a host of different halogenated by-products. When such by-products form during water treatment disinfection, these by-products, known as nitrogen-based disinfection by-products (N-DBPs), can be highly toxic and affect human and ecosystem health. Alternatively, when such reactions occur during membrane filtration, the organic nitrogen compounds, which are embedded within the upper layer polymer structure of the membrane filter, can degrade when free chlorine is applied. Therefore, this research was aimed at exploring the chemistry behind how specific types of organic nitrogen compounds which are found in these applications, such as tertiary amines and amides, react with free chlorine. It particularly focused on assessing the kinetics and by-product formation of these reactions under variable water quality conditions (e.g., pH, halide concentrations, and precursor doses).

More specifically, in the first phase of this work, the roles of tertiary amines in enhancing disinfection by-product (DBP) formation, such as trihalomethanes (THMs) and haloacetic acids (HAAs), during chlorination of aromatic compounds were studied. The results indicated that in synthetic solutions, chloroform (CHCl₃) and trichloroacetic acid (TCAA) were enhanced by up to 20× with tertiary amines at low dose ([tertiary amine]₀ = 0.5×[aromatic compound]₀). The enhancement effect was also dependent on the aromatic compound type, tertiary amine type and dose, and water conditions such as pH and bromide concentrations. Thus, THMs and HAAs were predicted to be enhanced when the aromatic compound reacted with R₃N-X⁺ (X=Br or Cl) and was not outcompeted by aromatic compound or tertiary amine reaction with free chlorine or bromine alone. In the second phase of this work, the reaction kinetics, by-product formation, and overall mechanisms of a polyamide-based monomer with chlorine were evaluated under varying water conditions. The current known mechanism, Orton Rearrangement, was reevaluated, and new mechanisms were proposed, where it was found that N-halogenation and ring halogenation were two independent pathways. The ability to choose either pathway was highly dependent on the water quality condition of the aqueous solution. The roles of different chlorinating/brominating agents were also investigated where certain species-specific rate constants were obtained. For the N-halogenation pathway, only chlorination and no bromination occurred in which the reactivity of the chlorinating agents likely decreased such that ClO^->HOCl. However, for the ring halogenation pathway, both chlorination and bromination occurred in which the reactivity of the chlorinating and brominating agents decreased such that Cl₂ >HOCl, and BrCl > BrOCl > Br₂ > Br₂O > HOBr, respectively. Overall, this study suggests that a number of unique reactions can occur for various types of organic nitrogen compounds which: (i) allow them to affect water quality by enhancing DBP formation, (ii) but, when integrated into a polymer matrix used for water treatment, can induce reactions that lead to permanent structural damage of the polymer. In all cases, the extent of these reactions is strongly governed by the surrounding water matrix.

Approximately 6.3 million bone fractures occur annually in the USA, resulting in considerable morbidity, deterioration in quality of life, loss of productivity and wages, and sometimes death (e.g. hip fractures). Although anabolic and antiresorptive agents have been introduced for treatment of osteoporosis, no systemically-administered drug has been developed to accelerate the fracture healing process. To address this need, we have undertaken to target a bone anabolic agent selectively to fracture surfaces in order to concentrate the drug’s healing power directly on the fracture site. We report here that conjugation of dasatinib to a bone fracture-homing oligopeptide via a releasable linker reduces fractured femur healing times in mice by ~60% without causing overt off-target toxicity or remodeling of nontraumatized bones. Thus, achievement of healthy bone density, normal bone volume, and healthy bone mechanical properties at the fracture site is realized after only 3-4 weeks in dasatinib-targeted mice, but requires ~8 weeks in PBS-treated controls. Moreover, optimizations have been implemented to the dosing regimen and releasing mechanisms of this targeted-dasatinib therapy, which has enabled us to cut the total doses by half, reduce the risk of premature release in circulation, and still improve upon the therapeutic efficacy. These efforts might reduce the burden associated with frequent doses on patients with broken bones and lower potential toxicity brought by drug degradation in the blood stream. In addition to dasatinib, a few other small molecules have also been targeted to fracture surfaces and identified as prospective therapeutic agents for the acceleration of fracture repair. In conclusion, in this dissertation, we have successfully targeted dasatinib to bone fracture surfaces, which can significantly accelerate the healing process at dasatinib concentrations that are known to be safe in oncological applications. A modular synthetic method has also been developed to allow for easy conversion of a bone-anabolic warhead into a fracture-targeted version for improved fracture repair.

In 2018, the World Health Organization (WHO) reported approximately 37 million people are living with the Human Immunodeficiency Virus (HIV). Suppressing replication of the virus down to undetectable levels was achieved by combination antiretroviral therapy (cART) which effectively reduced the mortality and morbidity rates of HIV positive individuals. Despite the improvements towards combatting HIV/AIDS, no successful treatment exists to eradicate the virus from an infected individual. Treatment regimens are lifelong and prompt less than desirable side effects including but not limited to; drug-drug interactions, toxicity, systemic organ complications, central nervous system HIV triggered disorders and most importantly, drug resistance. Current therapies are becoming ineffective against highly resistant HIV strains making the ability to treat long-term viral suppression a growing issue. Therefore, potent and more effective HIV inhibitors provide the best chance for long-term successful cART.

HIV-1 protease (PR) enzyme plays a critical role in the life cycle and replication of HIV. Significant advancements were achieved through structure-based design and X-ray crystallographic analysis of protease-bound to HIV-1 and brought about several FDA protease inhibitors (PI). Highly mutated HIV-1 variants create a challenge for current and future treatment regimens. This thesis work focuses on the design, synthesis, and evaluation of two new classes of potent HIV-1 PIs that exhibit a novel bicyclic oxazolidinone feature as the P2 ligand and a novel bis squaramide scaffold as the P2/P3 ligand. Several inhibitors displayed good to excellent activity toward HIV-1 protease and significant antiviral activity in MT-4 cells. Inhibitors 1.65g and 1.65h were further evaluated against a panel of highly resistant multidrug-resistant HIV-1 variants and displayed antiviral activity similar to Darunavir. X-ray crystal structures of inhibitor 1.65a and inhibitor 1.65i were co-crystallized with wild type HIV-1 protease and solved at a 1.22 Å and 1.30 Å resolution and maintained strong hydrogen bond with the backbone of the PR enzyme.

Recent trends in materials science have exploited noncovalent monolayer chemistries to modulate the physical properties of 2D materials, while minimally disrupting their intrinsic properties (such as conductivity and tensile strength). Highly ordered monolayers with pattern resolutions <10 nm over large scales are frequently necessary for device applications such as energy conversion or nanoscale electronics. Scanning probe microscopy is commonly employed to assess molecular ordering and orientation over nanoscopic areas of flat substrates such as highly oriented pyrolytic graphite, but routine preparation of high-quality substrates for device and other applications would require analyzing much larger areas of topographically rougher substrates such as graphene. In this work, we combine scanning electron microscopy with polarization modulated IR reflection adsorption spectroscopy to quantify the order of lying down monolayers of diynoic acids on few layer graphene and graphite substrates across areas of ~1 cm². We then utilize these highly ordered molecular films for templating assembly of di-peptide semiconductor precursors at the nanoscale, for applications in organic optoelectronic device fabrication.

A pigment is a finely divided solid colouring material, essentially insoluble in its application medium. Pigments are used mostly in the coloration of paints, printing inks and plastics. In contrast to textile dyes, where individual dye molecules are strongly attracted to individual polymer fibre molecules, pigments are considered to have only a weak affinity for their application medium. Pigments are incorporated to modify the optical properties of a substrate, the most obvious effect being to provide colour, however, this is not their only optical function; they can also provide opacity, high transparency, and a gloss effect. A pigment owes its optical properties to a combination of two effects that result from the interaction of the pigment particles with visible light: light absorption and light scattering. In chemical terms, pigments are classified as inorganic or organic. In general, inorganic pigments are high refractive index materials capable of providing high opacity, while organic pigments are of low refractive index and consequently are transparent. In addition to providing appropriate optical properties, pigments must be capable of withstanding the effects of the environment in which they are placed both during processing and in their anticipated lifetimes. They are required to be fast to light, weathering (if external exposure is envisaged), heat and chemicals such as acids and alkalis. Inorganic pigments are capable of providing excellent resistance to heat, light, weathering, solvents and chemicals. Organic pigments are characterised by high colour strength and brightness, although their fastness properties are somewhat variable. This chapter provides an overview of the characteristic structural features of the most important commercial pigments.

In contrast to the application of pigments, involving mechanical anchoring of discrete solid particles in a polymeric matrix, dyeing relies on equilibrium processes involving diffusion or sorption of dye molecules or ions within the substrate. Dyes are used in the coloration of a wide range of substrates including paper, leather and plastics, but by far their most important outlet is textiles. Textile fibres may be classified into three broad groups: natural, semi-synthetic and synthetic. These fibres share the common feature that they are made up of polymeric organic molecules; however, the physical and chemical natures of the polymers involved vary widely, explaining why each type of fibre essentially requires its own ‘tailor-made’ application classes of dyes. Since textile dyes are almost always applied from an aqueous dyebath solution, they are required to be soluble in water, or, alternatively, to be capable of conversion to a water-soluble form suitable for application. Dyes must firmly attach to the textile fibres to which they are applied in order to resist removal, for example by washing. The dye must distribute itself evenly throughout the material to give a uniform colour, referred to as a level dyeing. Finally, the dye must provide an appropriate range of fastness properties, for example to light, washing, heat, rubbing, etc. This chapter deals with the chemical principles underlying the main application classes of dyes that may be applied to textile fibres, with the exception of the reactive dye class.

Alcohols are usually protected as alkyl or silyl ethers. Michael P. Jennings of the University of Alabama found (Tetrahedron Lett. 2008, 49, 5175) that pyridinium tribromide can selectively remove the TBS (or TES) protection from the primary alcohol of a protected primary-secondary alcohol such as 1. Propargyl ethers are useful because they are stable, but can be selectively removed in the presence of other protecting groups. Shino Manabe and Yukishige Ito at RIKEN showed (Tetrahedron Lett. 2008, 49, 5159) that SmI2 could reductively remove a propargyl group in the presence of acetonides (illustrated, 3), MOM, benzyl and TBS ethers. Hisanaka Ito of the Tokyo University of Pharmacy and Life Sciences took advantage (Organic Lett. 2008, 10, 3873) of the reducing power of Cp2Zr to selectively remove the allyl ethers from 5, to give 6. These conditions might also remove propargyl ethers. Esters can also be useful protecting groups. Naoki Asao of Tohoku University developed (Tetrahedron Lett . 2008, 49, 7046) the o-alkynyl ester 7. Au catalyst in EtOH removed the ester, leaving benzoates, acetates, OTBS and OTHP intact. Alternatively, an o-iodobenzoate can be removed by Sonogashira coupling followed by the Au hydrolysis. N-Formylation is usually accomplished using mixed anhydrides. Weige Zhang and Maosheng Chang of Shenyang Pharmaceutical University put forward ( Chem. Commun. 2008 , 5429) an intriguing alternative, heating a secondary amine 9 with KCN in the presence of dimethyl malonate to give 10. Many of the current methods for amination that have been developed deliver the aryl amine. John F. Hartwig of the University of Illinois established (J. Am. Chem. Soc. 2008, 130, 12220) that exposure of the amine 11 to Boc2O followed by CAN led to the protected, dearylated amine 12. Adam McCluskey of The University of Newcastle observed (Tetrahedron Lett. 2008, 49, 6962) that microwave heating removed Boc protecting groups when there was a free carboxylic acid elsewhere in the molecule. Michael Lefenfeld of SiGNa Chemistry and James E. Jackson of Michigan State University used (Organic Lett. 2008, 10, 5441) easilyhandled Na/silica gel to remove primary and secondary sulfonamides (e.g. 15 → 16). Methanesulfonamides were also removed under these conditions.

Vitamins are essential organic nutrients required by animals in only tiny amounts. As animals have evolved they have come to rely on their diet to supply the metabolites now recognised as vitamins rather than synthesise them for themselves. Deficiencies cause specific deficiency syndromes. Vitamins are differentiated from various other dietary components: essential fatty acids and indispensable amino acids are required in larger amounts, trace metals are not organic, hormones are synthesised by the body as required rather than obtained from the diet and many other substances, while beneficial in the treatment of a particular illness do not invoke that illness when omitted from the diet. The history of vitamin discovery has led to often confusing nomenclature (B1, C, etc.). Vitamins are classified as either water soluble, i.e. thiamin, riboflavin, pyridoxine, pyridoxol, niacin, cobalamin, folic acid, biotin, pantothenic acid and ascorbic acid or fat soluble, i.e. retinol, cholecalciferol, vitamin E and vitamin K. The distribution of vitamins in foods, their physiological roles (including function at the biochemical level), and stability in food processing etc. are now well understood. The chapter concludes with a list of specialist books and review articles for further study.

The peptidomimetic-based design and synthesis of HIV-1 protease and other entry inhibitors are generally oriented to block the viral receptor functionalities in the host cells. Most of the drugs classified under HIV-1 protease inhibitors are primarily optimized through substrate-based design strategies. The peptidomimetic drugs present in the market are non-hydrolyzable by the catalytic aspartic acid residues, an indispensable approach still used in designing potential pharmacophores for protease inhibitors. Thus, a variety of amino acid-containing hybrid small molecules are tested against the HIV-1 protease enzyme by incorporating essential fragments required to block protease functionalities. However, the appearance of mutations in HIV polyproteins is a key parameter to be seriously considered while designing peptidomimetics. Hence, comprehensive knowledge regarding HIV peptidomimetic/medicinal chemistry along with optimization strategy and organic synthesis awareness is critical in the current scenario. The present chapter is aimed to provide in-depth literature on medicinally optimized HIV-1 protease inhibitors, Tat TAR RNA blockers with their synthesis, and later it is expanded to the peptidomimetics (entry inhibitors) involved in the envelope glycoprotein (gp120/gp41) and capsid inhibitors. Furthermore, the knowledge-based classification of HIV-1 protease inhibitors, anti-dimer agents, Tat-TAR RNA blockers, and entry inhibitors, along with their synthetic procedures, would serve as a single model template for scientific as well as academic research towards the development of anti-HIV peptidomimetics.

The control of microorganisms has always concerned food technologists. The fundamental biological similarities of bacteria, fungi etc. with humans can make “control” of food borne microorganisms rather than “elimination” a goal. Foodstuffs are ideal vehicles for microbial pathogens, degradative bacteria and fungi and the toxins they so often secrete. Heat, cold, reduced water activity and controlled atmospheres are largely outside the scope of this chapter, which concentrates on chemical techniques. Chemical preservatives inevitably have adverse effects on the physiology of micro-organisms so that possible adverse effects on consumers is a major issue. Sodium chloride has been a valued preservative since ancient times but nowadays its flavour is often as important as its effect on water activity. It is often used alongside nitrites and the biochemistry of nitrite's antimicrobial activity and interaction with muscle pigments is particularly complex. Smoking evolved from drying techniques but is now more important as a source of flavour. Sulfur dioxide, benzoates and other organic acids are most important for use with fruit based products. The antibiotics nisin and natamycin and ionising radiation have limited but valued applications. The chapter includes a detailed listing of the preservatives permitted as food additives in the EU, USA and elsewhere and concludes with a list of specialist books and review articles for further study.

Food colour has of far more than aesthetic importance. Colour is important in the identification of different foods, particularly fruit, and also helps establish ripeness or freshness in most food, including meat (see Chapter 4). Added colours, artificial or natural, can mask the effects of processing etc. and dishonestly mask the true identity of the ingredients of food products. The chemical properties of the natural pigments, chlorophylls (green), carotenoids (yellow, orange, red), anthocyanins (red, purple, blue), betalaines (beet pigments, red) and melanins (particularly in tea), are relevant to food processing and their usefulness as colorants. Other natural food colorants of note are turmeric, cochineal, safflower, sandalwood and malt extract. Colours extracted from microorganisms, e.g. the blue from Spirulina sp. are posing difficult regulatory questions. The number of synthetic dyestuffs (many but not all azo compounds) permitted as food colours has fallen steadily since the 1950s. The possible involvement of some with childhood behavioural disorders has overtaken concern over their potential carcinogenicity. The molecular basis of colour in organic molecules and the measurement of the colour of food materials are topics outside the consideration of particular food substances that concern food chemists. The chapter includes a detailed listing of the synthetic colours permitted in the EU, USA and elsewhere and concludes with a list of specialist books and review articles for further study.

The dioxides of titanium (TiO2), manganese (MnO2), and zirconium (ZrO2) are important materials because of their technological uses. TiO2 is used mainly as white pigment. Because of its semiconducting properties, TiO2, in its nanomaterial form, is also used as an active component of photocells and photocatalysis for self-cleaning glasses and cements . MnO2 is used primarily in electrode materials. ZrO2 is used in refractory ceramics, abrasive materials, and stabilized zirconia as ionic conductive materials stable at high temperature. Many of these properties are, of course, dependent on particle size and shape (§ Chap. 1). Dioxides of other tetravalent elements with interesting properties have been studied elsewhere in this book, especially VO2, which exhibits a metal–isolator transition at 68°C, used, for instance, in optoelectronics (§ 4.1.5), and silica, SiO2 (§ 4.1.4), which is likely the most ubiquitous solid for many applications and uses. Aqueous chemistry is of major interest in synthesizing these oxides in the form of nanoparticles from inorganic salts and under simple, cheap, and envi­ronmental friendly conditions. However, as the tetravalent elements have re­stricted solubility in water (§ 2.2), metal–organic compounds such as titanium and zirconium alkoxides are frequently used in alcoholic solution as precursors for the synthesis of TiO2 and ZrO2 nanoparticles. An overview of the conversion of alkoxides into oxides is indicated about silica formation (§ 4.1.4), and since well-documented works have already been published, these compounds are not considered here. The crystal structures of most MO2 dioxides are of TiO2 rutile type for hexacoordinated cations (e.g., Ti, V, Cr, Mn, Mo, W, Sn, Pb) and CaF2 fluorite type for octacoordinated, larger cations (e.g., Zr, Ce), but polymorphism is common. Some dioxides of elements such as chromium and tin form only one crystal­line phase. So, hydrolysis of SnCl4 or acidification of stannate [Sn(OH)6]2− leads both to the same rutile-type phase, cassiterite, SnO2. Many other dioxides are polymorphic, especially TiO2, which exists in three main crystal phases: anatase, brookite, and rutile; and MnO2, which gives rise to a largely diversified crystal chemistry.

Alkali metal GICs are the best known donor type GICs, since they are easily prepared and their brilliant gold color for stage-1 GICs has attracted scientists working in intercalation chemistry. They have therefore been targets of intensive and detailed studies of their solid-state properties on the basis of the employment of highly oriented pyrolytic graphite (HOPG). There are several intercalation methods, which are classified basically into vapor-phase reaction, reaction of the mixture of graphite and alkali metal, high pressure reaction, electrochemical reaction, and reaction in a solvent. Among these methods, vapor-phase intercalation reaction is the most popular. The two-zone method can easily give alkali metal GICs with well-defined single-stage phases. The vapor pressure of the alkali metal becomes high enough to obtain a satisfactory reaction rate for intercalation reaction in the temperature range 200-550°C, at which we can use a Pyrex glass tube as a reaction chamber. Figure 2.1 shows a typical two-zone method, where graphite and alkali metal are maintained at different temperatures, TG and TI, respectively, in a vacuum-sealed glass tube placed in a two-zone furnace. Changing TI controls the vapor pressure of the alkali metal. Figure 2.2 presents the conditions of intercalation reaction with potassium, where single-stage phase samples with stages 1 to 8 are obtained by changing the temperature difference TG — TK (Nishitani et al., 1983). Typical experimental conditions are given in Table 2.1 for the preparation of K, Rb, and Cs GICs (Dresselhaus and Dresselhaus, 1981). The intercalation reaction is again carried out by heating a mixture of graphite and alkali metal in a vacuum-sealed glass tube. In this case, the reaction becomes considerably more rapid owing to direct contact of molten alkali metal with graphite, although the reaction takes place in a similar manner to the vapor-phase reaction. A stainless steel tube is used for the intercalation of lithium since lithium vapor degrades a glass tube because of its high chemical activity. Alkali metal can be intercalated into graphite when the alkali metal is solvated in liquid ammonia or an organic solvent such as dimethylsulphoxide (DMSO).

One cannot overestimate the importance of oxygenated organic compounds in atmospheric chemistry. As discussed in the previous chapters of this book and elsewhere (e.g., Wayne, 1991; Seinfeld and Pandis, 1998; Brasseur et al., 1999; Finlayson-Pitts and Pitts, 2000; Calvert et al., 2000, 2002, 2008) the atmosphere is an oxidizing environment and all organic compounds emitted into the atmosphere are converted into oxygenated organic compounds. The first-generation products are oxidized further. As an example, the oxidation of ethane gives CH3CHO, C2H5OH, and C2H5OOH as first-generation products and CH3OH, CH3OOH, CH2O, and HC(O)OH as second-generation products. An understanding of the chemistry of oxygenated organic compounds is central to unraveling the complex processes in the atmosphere. In this chapter we discuss the representation of oxygenates in atmospheric models, their participation in secondary organic aerosol formation, contribution to HOx chemistry in the upper troposphere, role in the transport of pollutants, and use as proxies for volatile organic compound (VOC) emissions. A major application of the chemical kinetics and mechanisms of VOC oxidation is the development of an understanding of the chemistry occurring in the troposphere and the use of that understanding to predict and develop strategies which help to mitigate adverse changes in air quality and climate change. Such applications depend on the development of models that assess chemical impacts; chemical mechanisms lie at the heart of such models. The mechanisms can be very detailed, often termed explicit, in models where the aim is to understand the chemistry occurring in a small volume of air, for example, in an analysis of processes determining radical concentrations in field measurements. Such a mechanistic approach can also be used, with increased computer resources, when a trajectory approach is used to assess the coupled impacts of atmospheric transport and chemistry. An Eulerian approach to modeling both regional and global processes presents greater problems, because the chemical rate equations have to be solved for each species at each spatial grid point in the model; this severely limits the number of chemical species that can be incorporated realistically in the model.

Abstract The Middle Marrat reservoir of Jurassic age is a tight carbonate reservoir with vertical and horizontal heterogeneous properties. The variation in lithology, vertical and horizontal facies distribution lead to complicated reservoir characterization which lead to unexpected production behavior between wells in the same reservoir. Marrat reservoir characterization by conventional logging tools is a challenging task because of its low clay content and high-resistivity responses. The low clay content in Marrat reservoirs gives low gamma ray counts, which makes reservoir layer identification difficult. Additionally, high resistivity responses in the pay zones, coupled with the tight layering make production sweet spot identification challenging. To overcome these challenges, integration of data from advanced logging tools like Sidewall Magnetic Resonance (SMR), Geochemical Spectroscopy Tool (GST) and Electrical Borehole Image (EBI) supplied a definitive reservoir characterization and fluid typing of this Tight Jurassic Carbonate (Marrat formation). The Sidewall Magnetic resonance (SMR) tool multi wait time enabled T2 polarization to differentiate between moveable water and hydrocarbons. After acquisition, the standard deliverables were porosity, the effective porosity ratio, and the permeability index to evaluate the rock qualities. Porosity was divided into clay-bound water (CBW), bulk-volume irreducible (BVI) and bulk-volume moveable (BVM). Rock quality was interpreted and classified based on effective porosity and permeability index ratios. The ratio where a steeper gradient was interpreted as high flow zones, a gentle gradient as low flow zones, and a flat gradient was considered as tight baffle zones. SMR logging proved to be essential for the proper reservoir characterization and to support critical decisions on well completion design. Fundamental rock quality and permeability profile were supplied by SMR. Oil saturation was identified by applying 2D-NMR methods, T1/T2 vs. T2 and Diffusion vs. T2 maps in a challenging oil-based mud environment. The Electrical Borehole imaging (EBI) was used to identify fracture types and establish fracture density. Additionally, the impact of fractures to enhance porosity and permeability was possible. The Geochemical Spectroscopy Tool (GST) for the precise determination of formation chemistry, mineralogy, and lithology, as well as the identification of total organic carbon (TOC). The integration of the EBI, GST and SMR datasets provided sweet spots identification and perforation interval selection candidates, which the producer used to bring wells onto production.