PURE AND APPLIED CHEMISTRY

One story as part of the Global Conversation on Sustainability: dye adsorption studies using a novel bio-derived calcite material
Christian-Robinson S and Kerton FM
Many of the United Nations' Sustainable Development Goals (SDGs) can be addressed through chemistry. Researchers at Memorial University of Newfoundland, Canada, have been sharing their stories on September 25 for the past two years through the Global Conversation on Sustainability. This article describes the details of one of these stories. As the global population increases, food production including aquaculture is increasing to provide for this. At the same time, this means more waste is produced. Waste from aquaculture is often overlooked as a source of valuable chemicals. By-products from farming blue mussels () is dominated by shells rich in calcite. A 'soft' calcite material prepared from waste mussels, via a combination of heat and acetic acid treatment, was investigated for its adsorptive properties and its possible use in wastewater remediation. The adsorption of two cationic dyes, methylene blue and safranin-O, on this material were evaluated through isothermal and kinetic modelling. The adsorption systems for both methylene blue and safranin-O can best be described using Langmuir isotherms and the respective adsorption capacities were 1.81 and 1.51 mg/g. The adsorption process was dominated by pseudo-second order rate kinetics. Comparisons are made with other mollusc-derived materials reported to date.
The nitro to amine reduction: from millions of tons to single molecule studies
Scaiano JC, Wang B, Bourgonje CR and Yaghmaei M
Palladium nanostructures are interesting heterogeneous catalysts because of their high catalytic activity in a vast range of highly relevant reactions such as cross couplings, dehalogenations, and nitro-to-amine reductions. In the latter case, the catalyst Pd@GW (palladium on glass wool) shows exceptional performance and durability in reducing nitrobenzene to aniline under ambient conditions in aqueous solutions. To enhance our understanding, we use a combination of optical and electron microscopy, in-flow single molecule fluorescence, and bench chemistry combined with a fluorogenic system to develop an intimate understanding of Pd@GW in nitro-to-amine reductions. We fully characterize our catalyst using advanced microscopy techniques, providing deep insights into its catalytic performance. We also explore Pd cluster migration on the surface of the support under flow conditions, providing insights into the mechanism of catalysis. We show that even under flow, Pd migration from anchoring sites seems to be minimal over 4 h, with the catalyst stability assisted by APTES anchoring.
Room temperature X-ray absorption spectroscopy of metalloenzymes with drop-on-demand sample delivery at XFELs
Bogacz I, Makita H, Simon PS, Zhang M, Doyle MD, Chatterjee R, Fransson T, Weninger C, Fuller F, Gee L, Sato T, Seaberg M, Alonso-Mori R, Bergmann U, Yachandra VK, Kern J and Yano J
X-ray crystallography and X-ray spectroscopy using X-ray free electron lasers plays an important role in understanding the interplay of structural changes in the protein and the chemical changes at the metal active site of metalloenzymes through their catalytic cycles. As a part of such an effort, we report here our recent development of methods for X-ray absorption spectroscopy (XAS) at XFELs to study dilute biological samples, available in limited volumes. Our prime target is Photosystem II (PS II), a multi subunit membrane protein complex, that catalyzes the light-driven water oxidation reaction at the MnCaO cluster. This is an ideal system to investigate how to control multi-electron/proton chemistry, using the flexibility of metal redox states, in coordination with the protein and the water network. We describe the method that we have developed to collect XAS data using PS II samples with a Mn concentration of <1 mM, using a drop-on-demand sample delivery method.
Reactivity of electrophilic cyclopropanes
Eitzinger A and Ofial AR
Cyclopropanes that carry an electron-accepting group react as electrophiles in polar, ring-opening reactions. Analogous reactions at cyclopropanes with additional C2 substituents allow one to access difunctionalized products. Consequently, functionalized cyclopropanes are frequently used building blocks in organic synthesis. The polarization of the C1-C2 bond in 1-acceptor-2-donor-substituted cyclopropanes not only favorably enhances reactivity toward nucleophiles but also directs the nucleophilic attack toward the already substituted C2 position. Monitoring the kinetics of non-catalytic ring-opening reactions with a series of thiophenolates and other strong nucleophiles, such as azide ions, in DMSO provided the inherent S2 reactivity of electrophilic cyclopropanes. The experimentally determined second-order rate constants for cyclopropane ring-opening reactions were then compared to those of related Michael additions. Interestingly, cyclopropanes with aryl substituents at the C2 position reacted faster than their unsubstituted analogues. Variation of the electronic properties of the aryl groups at C2 gave rise to parabolic Hammett relationships.
My path in the company of chemistry
Baird BA
Experiencing the honor of this international recognition in chemistry, I wonder how this came to be. I reflect on my imperfect but rewarding path to where I am now, and on those who have helped me along the way.
Bioceramics: from bone substitutes to nanoparticles for drug delivery
Vallet-Regí M
Since the second half of the 20 century, bioceramics are used for bone repair and regeneration. Inspired by bones and teeth, and aimed at mimicking their structure and composition, several artificial bioceramics were developed for biomedical applications. And nowadays, in the 21 century, with the increasing prominence of nanoscience and nanotechnology, certain bioceramics are being used to build smart drug delivery systems, among other applications. This minireview will mainly describe both tendencies through the research work carried out by the research team of María Vallet-Regí.
Extending the -benzimidazolyl (SBiz) platform: -alkylated SBiz glycosyl donors with the universal activation profile
Hasty SJ, Rath NP and Demchenko AV
This article describes the development of alkylated -benzimidazolyl (SBiz) imidates as versatile building blocks for chemical glycosylation. The SBiz imidates have been originally developed as a new platform for active-latent glycosylations and its utility was further extended to other common strategies for oligosaccharide synthesis. This article expands upon the utility of these compounds. We developed a general protocol for the synthesis of a series of -alkylated SBiz glycosides from -protected SBiz aglycones by Lewis acid-mediated coupling with glucose pentaacetate. The -alkylated SBiz moiety was found to be stable under strong basic conditions which allowed us to obtain both armed and disarmed -alkylated SBiz donors. These donors showed good reactivity at a variety of activation conditions, and generally provided high yields in glycosylations.
Tailoring Trehalose for Biomedical and Biotechnological Applications
O'Neill MK, Piligian BF, Olson CD, Woodruff PJ and Swarts BM
Trehalose is a non-reducing sugar whose ability to stabilize biomolecules has brought about its widespread use in biological preservation applications. Trehalose is also an essential metabolite in a number of pathogens, most significantly the global pathogen , though it is absent in humans and other mammals. Recently, there has been a surge of interest in modifying the structure of trehalose to generate analogues that have applications in biomedical research and biotechnology. Non-degradable trehalose analogues could have a number of advantages as bioprotectants and food additives. Trehalose-based imaging probes and inhibitors are already useful as research tools and may have future value in the diagnosis and treatment of tuberculosis, among other uses. Underlying the advancements made in these areas are novel synthetic methods that facilitate access to and evaluation of trehalose analogues. In this review, we focus on both aspects of the development of this class of molecules. First, we consider the chemical and chemoenzymatic methods that have been used to prepare trehalose analogues and discuss their prospects for synthesis on commercially relevant scales. Second, we describe ongoing efforts to develop and deploy detectable trehalose analogues, trehalose-based inhibitors, and non-digestible trehalose analogues. The current and potential future uses of these compounds are discussed, with an emphasis on their roles in understanding and combatting mycobacterial infection.
3-Acyloxy-1,4-enyne: a New Five-carbon Synthon for Rhodium-Catalyzed (5+2) Cycloadditions
Schienebeck CM, Li X, Shu XZ and Tang W
Seven-membered rings are ubiquitous in natural products and pharmaceutical agents and their syntheses continue to stimulate the development of novel synthetic methods. The (5+2) cycloaddition is one of the most efficient ways to access seven-membered rings since the 2-carbon components (alkenes, alkynes, or allenes) are readily available. Prior to our study, however, there was only one type of transition metal-catalyzed (5+2) cycloaddition: the reaction between vinylcyclopropanes and alkenes, alkynes, or allenes. We recently developed a new type of transition metal-catalyzed (5+2) cycloaddition, where the 5-carbon building block is 3-acyloxy-1,4-enyne (ACE). Our recent progress on Rh-catalyzed intra- and intermolecular (5+2) cycloadditions of ACEs and alkynes is summarized in this article. Using chiral propargylic esters, bicyclic products were prepared in high optical purity by the intramolecular (5+2) cycloadditions. Monocyclic seven-membered rings were synthesized by intermolecular (5+2) cycloaddition of ACEs and alkynes. Kinetic studies indicated that the rate of this intermolecular cycloaddition was significantly accelerated when the acetate was replaced by dimethylaminobenzoate. DFT calculations suggested that novel metallacycles were generated by a Rh-promoted oxidative cycloaddition of 1,4-enynes accompanied by a 1,2-acyloxy migration of propargylic esters.
New ligand platforms featuring boron-rich clusters as organomimetic substituents
Spokoyny AM
200 years of research with carbon-rich molecules have shaped the development of modern chemistry. Research pertaining to the chemistry of boron-rich species has historically trailed behind its more distinguished neighbor (carbon) in the periodic table. Notably, a potentially rich and, in many cases, unmatched field of coordination chemistry using boronrich clusters remains fundamentally underdeveloped. Our work has been devoted to examining several basic concepts related to the functionalization of icosahedral boron-rich clusters and their use as ligands, aimed at designing fundamentally new hybrid molecular motifs and materials. Particularly interesting are icosahedral carboranes, which can be regarded as 3D analogs of benzene. These species comprise a class of boron-rich clusters that were discovered in the 1950s during the "space race" while researchers were developing energetic materials for rocket fuels. Ultimately, the unique chemical and physical properties of carborane species, such as rigidity, indefinite stability to air and moisture, and 3D aromaticity, may allow one to access a set of properties not normally available in carbon-based chemistry. While technically these species are considered as inorganic clusters, the chemical properties they possess make these boron-rich species suitable for replacing and/or altering structural and functional features of the organic and organometallic molecules-a phenomenon best described as "organomimetic". Aside from purely fundamental features associated with the organomimetic chemistry of icosahedral carboranes, their use can also provide new avenues in the development of systems relevant to solving current problems associated with energy production, storage, and conversion.
Stereocontrolled 1--glycosylation and comparative binding studies of photoprobe-thiosaccharide conjugates with their -linked analogs
Deng L, Wang X, Uppalapati S, Norberg O, Dong H, Joliton A, Yan M and Ramström O
The use of thioglycosides and other glycan derivatives with anomeric sulfur linkages is gaining increasing interest, both in synthesis and in various biological contexts. Herein, we demonstrate the occurrence and circumvention of anomerization during 1--glycosylation reactions, and present highly efficient and stereocontrolled syntheses of a series of photoprobe-thiosaccharide conjugates. Mutarotation of glycosyl thiols proved to be the origin of the anomeric mixtures formed, and kinetic effects could be used to circumvent anomerization. The synthesized carbohydrate conjugates were then evaluated by both solution- and solid-phase-based techniques. Both binding results showed that the -linked glyco-sides interact with their cognate lectins comparably to the corresponding -analogs in the present cases, thus demonstrating the reliability of the solid-support platform built upon our photo-initiated carbohydrate immobilization method for probing protein bindings, and showing the potential of combining these two means for studying carbohydrate-protein interactions.
Progress toward red and near-infrared (NIR) emitting saccharide sensors
Sibrian-Vazquez M, Escobedo JO, Lowry M and Strongin RM
Red-shifted and near-infrared (NIR)-active rhodamine analogs and their boronic acid derivatives were synthesized and studied. These latter compounds function as fluorogenic NIR active substrates for sugar sensing. The effects of benzannulation and boronic acid functionalization on fluorophore optical and sensing properties are described.
Balancing life with glycoconjugates: monitoring unfolded protein response-mediated anti-angiogenic action of tunicamycin by Raman Spectroscopy
Longas MO, Kotapati A, Prasad KP, Banerjee A, Santiago J, Baksi K and Banerjee DK
Asparagine-linked protein glycosylation is a hallmark for glycoprotein structure and function. Its impairment by tunicamycin [a competitive inhibitor of N-acetylglucosaminyl 1-phosphate transferase (GPT)] has been known to inhibit neo-vascularization (i.e., angiogenesis) in humanized breast tumor due to an induction of ER stress-mediated unfolded protein response (UPR). The studies presented here demonstrate that (i) tunicamycin (i) inhibits capillary endothelial cell proliferation in a dose dependent manner; (ii) treated cells are incapable of forming colonies upon its withdrawal; and (iii) tunicamycin treatment causes nuclear fragmentation. Tunicamycin-induced ER stress-mediated UPR event in these cells was studied with the aid of Raman spectroscopy, in particular, the interpretation of bands at 1672, 1684 and 1694 cm(-1), which are characteristics of proteins and originate from C=O stretching vibrations of mono-substituted amides. In tunicamycin-treated cells these bands decreased in area as follows: at 1672 cm(-1) by 41.85% at 3 h and 55.39% at 12 h; at 1684 cm(-1) by 20.63% at 3 h and 40.08% at 12 h; and also at 1994 cm(-1) by 33.33% at 3 h and 32.92% at 12 h, respectively. Thus, in the presence of tunicamycin, newly synthesized protein chains fail to arrange properly into their final secondary and/or tertiary structures, and the random coils they form had undergone further degradation.
Synthesis of Lipid A and Inner Core LPS ligands containing 4-amino-4-deoxy-l-arabinose units
Zamyatina A, Hollaus R, Blaukopf M and Kosma P
Attachment of 4-amino-4-deoxy-l-arabinose to phosphates or sugar hydroxyl groups of lipopolysaccharide contributes to bacterial resistance against common antibiotics. For a detailed study of antigenic properties and binding interactions, Ara4N-containing inner core ligands related to Burkholderia and Proteus LPS have been synthesized in good yields. Glycosylation at position 8 of allyl glycosides of oct-2-ulosonic acids (Ko, Kdo) has been accomplished using an N-phenyltrifluoroacetimidate 4-azido-4-deoxy-l-arabinosyl glycosyl donor followed by azide reduction and global deprotection. The β-l-Ara4N-(1→8)-α-Kdo disaccharide was further extended into the branched β-l-Ara4N-(1→8)[α-Kdo-(2→4)]-α-Kdo trisaccharide via a regioselective glycosylation of a protected triol intermediate. Synthesis of Ara4N-modified lipid A - part structure occurring in the LPS of Burkholderia, Pseudomonas and Klebsiellla strains was accomplished using the H-phosphonate approach. The stereocontrolled assembly of the phosphodiester linkage connecting glycosidic centres of two aminosugars was elaborated employing an anomeric H-phosphonate of cyclic silyl-ether protected 4-azido-4-deoxy-β-l-arabinose which was coupled to the hemiacetal of the lipid A GlcN-disaccharide backbone. Conditions for global deprotection which warrant the integrity of "double anomeric" phosphodiester linkage were successfully developed. Introduction of thiol-terminated spacer at the synthetic ligands allows both coupling to BSA and immobilization on gold nanoparticles as well as generation of glycoarrays.
Recent advances in analysis of trace elements in environmental samples by X-ray based techniques (IUPAC Technical Report)
Terzano R, Denecke MA, Falkenberg G, Miller B, Paterson D and Janssens K
Trace elements analysis is a fundamental challenge in environmental sciences. Scientists measure trace elements in environmental media in order to assess the quality and safety of ecosystems and to quantify the burden of anthropogenic pollution. Among the available analytical techniques, X-ray based methods are particularly powerful, as they can quantify trace elements . Chemical extraction is not required, as is the case for many other analytical techniques. In the last few years, the potential for X-ray techniques to be applied in the environmental sciences has dramatically increased due to developments in laboratory instruments and synchrotron radiation facilities with improved sensitivity and spatial resolution. In this report, we summarize the principles of the X-ray based analytical techniques most frequently employed to study trace elements in environmental samples. We report on the most recent developments in laboratory and synchrotron techniques, as well as advances in instrumentation, with a special attention on X-ray sources, detectors, and optics. Lastly, we inform readers on recent applications of X-ray based analysis to different environmental matrices, such as soil, sediments, waters, wastes, living organisms, geological samples, and atmospheric particulate, and we report examples of sample preparation.
First total synthesis of the (±)-2-methoxy-6-heptadecynoic acid and related 2-methoxylated analogs as effective inhibitors of the leishmania topoisomerase IB enzyme
Carballeira NM, Cartagena M, Li F, Chen Z, Prada CF, Calvo-Alvarez E, Reguera RM and Balaña-Fouce R
The fatty acids (±)-2-methoxy-6Z-heptadecenoic acid (1), (±)-2-methoxy-6-heptadecynoic acid (2) and (±)-2-methoxyheptadecanoic acid (3) were synthesized and their inhibitory activity against the Leishmania DNA topoisomerase IB enzyme (LdTopIB) determined. Acids 1 and 2 were synthesized from 4-bromo-1-pentanol, the former in ten steps and in 7% overall yield, while the latter in seven steps and in 14% overall yield. Acid 3 was prepared in six steps and in 42% yield from 1-hexadecanol. Acids 1-3 inhibited the LdTopIB enzyme following the order 2 > 1 ⪢ 3, with 2 displaying an EC(50) = 16.6 ± 1.1 μM and 3 not inhibiting the enzyme. Acid 1 preferentially inhibited the LdTopIB enzyme over the human TopIB enzyme. Unsaturation seems to be a prerequisite for effective inhibition, rationalized in terms of weak intermolecular interactions between the active site of LdTopIB and either the double or triple bonds of the fatty acids. Toxicity towards Leishmania donovani promastigotes was also investigated resulting in the same order 2 > 1 > 3, with 2 displaying an EC(50) = 74.0 ± 17.1 μM. Our results indicate that α-methoxylation decreases the toxicity of C(17:1) fatty acids towards L. donovani promastigotes, but improves their selectivity index.
Chemical data evaluation: general considerations and approaches for IUPAC projects and the chemistry community (IUPAC Technical Report)
Shaw DG, Bruno I, Chalk S, Hefter G, Hibbert DB, Hutchinson RA, Magalhães MCF, Magee J, McEwen LR, Rumble J, Russell GT, Waghorne E, Walczyk T and Wallington TJ
The International Union of Pure and Applied Chemistry (IUPAC) has a long tradition of supporting the compilation of chemical data and their evaluation through direct projects, nomenclature and terminology work, and partnerships with international scientific bodies, government agencies and other organizations. The IUPAC Interdivisional Subcommittee on Critical Evaluation of Data (ISCED) has been established to provide guidance on issues related to the evaluation of chemical data. In this first report we define the general principles of the evaluation of scientific data and describe best practices and approaches to data evaluation in chemistry.
Formation of C-C bonds via ruthenium-catalyzed transfer hydrogenation()
Moran J and Krische MJ
Ruthenium-catalyzed transfer hydrogenation of diverse π-unsaturated reactants in the presence of aldehydes provides products of carbonyl addition. Dehydrogenation of primary alcohols in the presence of the same π-unsaturated reactants provides identical products of carbonyl addition. In this way, carbonyl addition is achieved from the alcohol or aldehyde oxidation level in the absence of stoichiometric organometallic reagents or metallic reductants. In this account, the discovery of ruthenium-catalyzed C-C bond-forming transfer hydrogenations and the recent development of diastereo- and enantioselective variants are discussed.
Good Reporting Practice for Thermophysical and Thermochemical Property Measurements (IUPAC Technical Report)
Bazyleva A, Abildskov J, Anderko A, Baudouin O, Chernyak Y, de Hemptinne JC, Diky V, Dohrn R, Richard JE, Jacquemin J, Jaubert JN, Joback KG, Kattner UR, Kontogeorgis G, Loria H, Mathias PM, O'Connell JP, Schröer W, Smith GJ, Soto A, Wang S and Weir RD
Scientific projects frequently involve measurements of thermophysical, thermochemical, and other related properties of chemical compounds and materials. These measured property data have significant potential value for the scientific community, but incomplete and inaccurate reporting often hampers their utilization. The present IUPAC Technical Report summarizes the needs of chemical engineers and researchers as consumers of these data and shows how publishing practices can improve information transfer. In the Report, general principles of are developed together with examples illustrating typical cases of reporting issues. Adoption of these principles will improve the quality, reproducibility, and usefulness of experimental data, bring a better level of consistency to results, and increase the efficiency and impact of research. Closely related to , basic elements of are also introduced with a goal to reduce the number of ambiguities and unresolved problems within the thermophysical property data domain.
Narratives of Undergraduate Research, Mentorship, and Teaching at UCLA
Stevens SL, Phung AC, Gonzalez A, Shao Y, Moully EH, Nguyen VT, Martin JL, Mao C, Saebi A, Mosallaei D, Kirollos M, Chong P, Umanzor A, Qian K, Marin G, Ebrahim OM, Pathuri RS, Hopp M, Ramachandran R, Waddington MA and Spokoyny AM
This work describes select narratives pertaining to undergraduate teaching and mentorship at UCLA Chemistry and Biochemistry by Alex Spokoyny and his junior colleagues. Specifically, we discuss how individual undergraduate researchers contributed and jump-started multiple research themes since the conception of our research laboratory. This work also describes several recent innovations in the inorganic and general chemistry courses taught by Spokoyny at UCLA with a focus of nurturing appreciation for research and creative process in sciences including the use of social media platforms.
Reference Materials for Phase Equilibrium Studies. 1. Liquid-Liquid Equilibria (IUPAC Technical Report)
Bazyleva A, Acree WE, Chirico RD, Diky V, Hefter GT, Jacquemin J, Magee JW, O'Connell JP, Olson JD, Polishuk I, Schmidt KAG, Shaw JM, Trusler JPM and Weir RD
This article is the first of three projected IUPAC Technical Reports resulting from IUPAC Project 2011-037-2-100 (Reference Materials for Phase Equilibrium Studies). The goal of that project was to select reference systems with critically evaluated property values for the validation of instruments and techniques used in phase equilibrium studies for mixtures. This Report proposes seven systems for liquid-liquid equilibrium studies, covering the four most common categories of binary mixtures: aqueous systems of moderate solubility, non-aqueous systems, systems with low solubility, and systems with ionic liquids. For each system, the available literature sources, accepted data, smoothing equations, and estimated uncertainties are given.