Chemical Literature Research Articles

Marine chemical ecology in benthic environments.

Covering: Most of 2013 up to the end of 2015 This review highlights the 2013-2015 marine chemical ecology literature for benthic bacteria and cyanobacteria, macroalgae, sponges, cnidarians, molluscs, other benthic invertebrates, and fish.

Searching for the best conditions

Organic Chemistry The vastness of the archival chemistry literature is both a blessing and a curse. The reaction that you're looking for is probably in there, provided you take enough time to search for it. Gao et al. trained a neural network model on 10 million known reactions to speed up this process. Specifically, the model was charged with predicting a catalyst, reagents, solvents, and temperature to achieve a given transformation. When tested, the model's top-10 list of suggestions produced a close match to actual conditions nearly 70% of the time, with a ±20°C error margin in temperature. ACS Cent. Sci. 4 , 1465 (2018).

Organic synthesis in a modular robotic system driven by a chemical programming language

The synthesis of complex organic compounds is largely a manual process that is often incompletely documented. To address these shortcomings, we developed an abstraction that maps commonly reported methodological instructions into discrete steps amenable to automation. These unit operations were implemented in a modular robotic platform by using a chemical programming language that formalizes and controls the assembly of the molecules. We validated the concept by directing the automated system to synthesize three pharmaceutical compounds, diphenhydramine hydrochloride, rufinamide, and sildenafil, without any human intervention. Yields and purities of products and intermediates were comparable to or better than those achieved manually. The syntheses are captured as digital code that can be published, versioned, and transferred flexibly between platforms with no modification, thereby greatly enhancing reproducibility and reliable access to complex molecules.

Sulfur Chemistry in Polymer and Materials Science.

Sulfur and its functional groups are major players in an area of exciting research taking place in modern polymer and materials science, both in academia and industry. In fact, manifold sulfur-based reactions that are both exceptionally versatile as well as tremendously useful have been implemented, and further utilized for the design and preparation of polymeric materials that lead to a plethora of applications ranging from medicine to optics and nanotechnology to separation science. Hence, within this review, an overview of strategies and developments used over the last 5 years to reinforce the importance of the sulfur functional group in modern polymer and materials science is presented. In particular, many important references in the primary literature of sulfur chemistry are referred to, including thiol-ene, thiol-yne, thiol-Michael addition, disulfide cross-linking, and thiol-disulfide exchange, among others, by explaining and illustrating the important principles. Last but not least, the grand aim to underpin the importance of sulfur in modern polymer and materials science is achieved by presenting selected examples in diverse fields and postulating the respective potential for real-world applications.

Higher-order cycloaddition reactions: A computational perspective

Higher-order cycloaddition reactions are more common in the chemical literature now than ever before. With this class of reactions, we see a prime example of experimental and computational science working together to drive innovation. Here, we present a brief overview of some of the computational developments with a focus on how this work has driven experiment and vice versa.

Cucurbit[8]uril (CB[8])-Based Supramolecular Switches.

The use of cucurbit[8]uril as a molecular host has emerged in the chemical literature as a reliable strategy for the creation of dynamic chemical systems, owing to its ability to form homo- and heteroternary complexes in aqueous media with appropriate molecular switches as guests. In this manner, CB[8]-based supramolecular switches can be designed in a predictable and modular fashion, through the selection of appropriate guests able to condition the redox, photochemical, or pH-triggered behavior of tailored multicomponent systems. Furthermore, CB[8] allows the implementation of dual/triple and linear/orthogonal stimuli-dependent properties into these molecular devices by a careful selection of the guests. This versatility in their design gives these supramolecular switches great potential for the rational development of new materials, in which their function is not only determined by the custom-made stimuli-responsiveness, but also by the transient aggregation/disaggregation of homo- or heteromeric building blocks.

Cyclooxygenase-1 (COX-1) and COX-1 Inhibitors in Cancer: A Review of Oncology and Medicinal Chemistry Literature.

Prostaglandins and thromboxane are lipid signaling molecules deriving from arachidonic acid by the action of the cyclooxygenase isoenzymes COX-1 and COX-2. The role of cyclooxygenases (particularly COX-2) and prostaglandins (particularly PGE2) in cancer-related inflammation has been extensively investigated. In contrast, COX-1 has received less attention, although its expression increases in several human cancers and a pathogenetic role emerges from experimental models. COX-1 and COX-2 isoforms seem to operate in a coordinate manner in cancer pathophysiology, especially in the tumorigenesis process. However, in some cases, exemplified by the serous ovarian carcinoma, COX-1 plays a pivotal role, suggesting that other histopathological and molecular subtypes of cancer disease could share this feature. Importantly, the analysis of functional implications of COX-1-signaling, as well as of pharmacological action of COX-1-selective inhibitors, should not be restricted to the COX pathway and to the effects of prostaglandins already known for their ability of affecting the tumor phenotype. A knowledge-based choice of the most appropriate tumor cell models, and a major effort in investigating the COX-1 issue in the more general context of arachidonic acid metabolic network by using the systems biology approaches, should be strongly encouraged.

Cation−Π Interactions in Biochemistry: A Primer

Although the potent effects of cation−π interactions for stabilizing protein structure and binding ligands to proteins have been reported in the chemical literature for over two decades, there are no undergraduate biochemistry textbooks covering this important noncovalent attractive force. In an attempt to remedy this situation, this primer describes what cation−π interactions are, provides biochemical examples of cation−π interactions that supplement the protein structure and ligand binding topics of a traditional one-semester biochemistry course, and offers exercises and worked out solutions on cation−π interactions derived from the biochemical literature. In addition, instructions are provided for using the online molecular visualization tools FirstGlance and JSmol viewer to identify cation−π interactions in proteins and for calculating cation−π stabilization energy with the online CaPTURE program.

Lichen diversity in geothermal area of Kamojang, Bandung, West Java, Indonesia and its potential for medicines and dyes

Kusmoro J, Noer IS, Jatnika MF, Permatasari RE, Partasasmita R. 2018. Lichen diversity in geothermal area of Kamojang, Bandung, West Java, Indonesia and its potential for medicines and dyes. Biodiversitas 19: 2335-2343. The study of lichens diversity in Kamojang, West Java was conducted by survey in geothermal field area following the line transect 6 km along to the East, North West and south from the Power House of Geothermal Power Plant. The lichen samples were taken from bark, soil, and stone. Lichen identification was done by morphological, anatomy and chemical analysis. Dyes potency of Parmotrema and Usnea test using ammoniac fermentation was done in Plant Taxonomy Laboratory of Department Biology, Faculty of Mathematics and Natural Sciences, University of Padjadjaran. The survey has successfully collected 133 species of lichens, belong to 62 genera and 17 families. Parmeliaceae was found as dominant groups, consisting of 33 species and other co-dominant groups are Graphidaceae and Lobariaceae with 24 species and 8 species, respectively. Most lichens in Kamojang geothermal area belong to Ascomycetes, only one Basidiomycetes such as Dictyonema sericeum (Sw.) which found at Kawah Manuk (Manuk crater) area. The rare species of lichens such as Usnea longissima Ach, was found at Pine forest in Arboretum 6 km south of Powerhouse of Kamojang geothermal. Chemical analysis and literature study for Lichenic acid contains was done and generally, atranorin, usnic acid, barbatic and lecanoric acid was found in lichens samples. Amoniac fermentation result showed that Parmotrema tinctorum produced brownish red, red and purple, which occurred within 1 week to 5 weeks after fermentation. While Usnea produced variety of brown color, which occurred within 5 days up to 4 weeks after fermentation. Lichen species containing some medical properties are Bulbothrix, Cladonia and Usnea. While lichens having dyes properties are Hypogymnia, Lobaria, Peltigera, Usnea, and Parmotrema.

Naphthol Green – a forgotten artists’ pigment of the early 20th century. History, chemistry and analytical identification

Abstract The synthetic nitroso dyestuff Acid Green 1 (hereafter AG1, C.I. 10020) and its lake (C.I. Pigment Green 12, hereafter PG12), today known under the trade name Naphthol Green B, was identified for the first time on six historical colour charts of commercial brands of artists’ paints. These comprise water and oil colours produced between 1910 and 1932 by the companies Winsor & Newton (London), G. Wagner (Hannover), Fr. Schoenfeld (Dusseldorf), Redeker & Hennis (Nurnberg) and Talens & Zoon (Apeldoorn). Because the use of AG1 (first synthesis in 1883) is well-known for textile dyeing, but not at all as a lake pigment for artists’ paints, these findings stimulated a comprehensive source research on the early production history, fastness properties and acceptance of the lakes of AG1 in the chemical and paint-technological literature from its invention to c. 1950. To summarize the findings, lakes of AG1 are regularly mentioned for paint purposes soon after the dyestuff's invention, mainly for house paints, paints for wall papers or as pigment for printing inks. In 1892, a lead lake of AG1 is described explicitly also for artists’ paints and a certain use in artists’ water colours, but also oil paints of higher quality could be proved until at least the 1930ies by the source research presented here. However, the pigment's fastness to light is unsatisfactory according to modern standards, and lakes of AG1, since 1956 denoted as PG12 (barium lake), are no longer of relevance in artists’ paints. It was presumably replaced by more stable organic green pigments such as those from the copper phthalocyanine group that have been introduced since the mid-1930ies. In this work, the non-destructive or minimally invasive analytical identification of AG1/PG12 in works of art is shown to be possible by Raman spectroscopy, SERS, FTIR and/or UV/VIS/NIR reflectance spectroscopy, accomplished by XRF for the lake substrate characterisation. Reference spectra of modern and historical specimens of AG1 (as lake and dye) produced in 1893 and 1900 are also presented here. Knowledge of the application and chronology of this today almost unknown pigment in art is of importance e.g. for dating purposes in authentication cases as well as under preventive conservation aspects, e.g. to define appropriate conditions for lightning conditions.

Comment on “Volumetric and compressibility behavior of l-valine in aqueous poly ethylene glycol solutions at T = (298.15, 308.15 and 318.15) K”

Search of the chemical literature reveals that the limiting apparent molal volumes for l-valine dissolved in water differ significantly from published literature values. The calculated limiting apparent molal volumes reported by Moradian and coworkers [J. Mol. Liq., in press, doi:https://doi.org/10.1016/j.molliq.2018.08.027] were φvo = −145.8768 cm3 mol−1 and φvo = −273.5163 cm3 mol–1 at 308.15 K and 318.15 K, respectively. Published literature values were in the range of about φvo = 90 cm3 mol−1 to φvo = 92 cm3 mol−1.

On the hydrolysis mechanisms of amides and peptides

AbstractHere the possibility is raised that peptide hydrolysis, in the absence of catalysis by proteases or buffers, may still have a self‐catalyzing mechanism that differs from ordinary amide hydrolysis. Second, an attempt is made to clarify the ongoing confusion in the computational chemistry literature regarding the rate‐limiting step in ordinary amide hydrolysis. Third, Gibbs activation energies (free‐energy barriers) for formamide hydrolysis are derived from rate constants and presented under different concentration conventions, for ease of comparison to values from computational chemistry predictions past and future.

A microscopic computer vision algorithm for autonomous bubble detection in aerated complex liquids

The size distribution of bubbles in cake batters is often determined from optical microscopic imaging, considering the lesser availability and non-affordability of sophisticated techniques such as light scattering, and acoustic methods. We present an automated bubble detection and counting method from microscopic images that presents flexibility and robustness over existing manual approaches. The method is able to successfully resolve connected bubbles and recognise far many bubbles in an image than would be possible by naked eye or hitherto reported methods in chemical and food engineering literature. Furthermore, the size data obtained for the bubbles can easily be used for routine statistical analysis. We demonstrate the application of our method for studying the influence of two different mixer geometries and three different speeds on bubble size.

Special issue: Plasma and Liquids

Special issue: Plasma and Liquids

Mass Spectrometry of Algal Chlorophyll c Compounds

Background: The term chlorophyll c encompasses a small but heterogeneous group of algal pigments, characterized for being porphyrins rather than chlorins. Chlorophylls c are protochlorophyllide-type compounds that differ in their peripheral substituents. Mass spectrometry has contributed to the structural elucidation of chlorophylls c, often in parallel with the development of soft ionization techniques. Objective: To provide comprehensive information on the structural characterization of chlorophylls c by mass spectrometry. Method: A detailed exam of the existing bibliography from both the chemical and marine science literatures followed by the analysis of data on molecular masses and product ions. Previous tandem mass spectra of chlorophyll c pigments are reproduced employing high resolution mass spectrometry. Results: This article reviews the application of direct and tandem mass spectrometry techniques to the analysis of acidic and esterified chlorophylls c, summarizes their fragmentation patterns and enumerates some experimental fragmentation rules for their identification. The high resolution mass spectra of acidic and esterified chlorophyll c compounds are shown as characteristic examples. Conclusion: The combined information on the molecular mass and diagnostic fragmentation allows the unambiguous characterization of the known acidic chlorophylls c, including the discrimination of isomeric pigments. Tandem mass spectrometry is a technique of choice for the study of galactolipid-esterified chlorophylls c, as the systematic fragmentation of successive parts in the molecules allows good tentative approaches to their structures. Keywords: Algae, chlorophylls c, chlorophyll c-galactoglyceride esters, fragmentation, mass spectrometry, protochlorophyllide, tandem mass spectrometry.

Revisiting the Scale-Invariant, Two-Dimensional Linear Regression Method

The scale-invariant way to analyze two-dimensional experimental and theoretical data with statistical errors in both the independent and dependent variables is revisited by using what we call the triangular linear regression method. This is compared to the standard least-squares fit approach by applying it to typical simple sets of example data from the actual chemical literature. A new add-in for Microsoft Excel, LinEstXY, and ready-to-use formulas for the scale-invariant method are provided.

Inosine 5'-Monophosphate Dehydrogenase (IMPDH) as a Potential Target for the Development of a New Generation of Antiprotozoan Agents.

Inosine-5'-monophosphate dehydrogenase (IMPDH) is a metabolic enzyme that catalyzes the critical step in guanine nucleotide biosynthesis, and thus is at the center of cell growth and proliferation. However, although this enzyme has been exploited as potential target for the development of immunosuppressive, anticancer, and antiviral agents, the functional importance of IMPDH as a promising antiprotozoan drug target is still in its infancy mainly because of the availability of alternative nucleotides metabolic pathways in many of these parasites. This situation suggests that the inhibition of IMPDH might have little to no effect on the survival of protozoan parasites. As a result, no IMPDH inhibitor is currently commercially available or has advanced to clinical trials as a potential antiprotozoan drug. Nevertheless, recent advances toward the development of selective inhibitors of the IMPDH enzyme from Crystosporidium parvum as potential drug candidates against cryptosporidiosis should revive further investigations of this drug target in other protozoa parasites. The current review examines the chemical structures and biological activities of reported protozoan's IMPDH inhibitors. SciFinder was used to broadly pinpoint reports published on the topic in the chemical literature, with no specific time frame. Opportunities and challenges towards the development of inhibitors of IMPDH enzymes from protozoa parasites as potential chemotherapies toward the respective diseases they cause are also discussed.

(Invited) Thermodynamic Aspects of Devices for Solar Energy and Chemical Conversions

The chemical literature does not strongly differentiate between photocatalytic (PC) and photosynthetic (PS) reactions (including artificial photosynthesis), even though these are different processes. Photocatalytic processes are thermodynamically downhill (ΔG<0) and are merely accelerated by a catalyst whereas photosynthetic processes are thermodynamically unfavorable (ΔG>0) and require photochemical energy input to occur. Here we apply this differentiation to formulate design criteria for PC and PS devices, with a special emphasis on solar water photoelectrolysis / solar hydrogen generation. As will be shown, under conditions of optimal light absorption, carrier lifetimes, and electrochemical rates, the performance of PCs is limited only by their surface area, while type 1 PS devices are limited by their carrier mobility and mass transport, and type 2 PS devices are limited by electrochemical charge-transfer selectivity. Strategies for the optimization of type 1 and 2 photosynthetic devices and photocatalysts are also discussed. Figure 1

Reactions

OPINION Reactions ShareShare onFacebookTwitterWechatLinked InRedditEmail C&EN, 2018, 96 (9), p 2February 26, 2018Cite this:C&EN 96, 9, 2Letters to the editor Palytoxin We read with interest Emma Hiolski’s article entitled “Palytoxin: The danger hidden in tropical aquariums” that described palytoxin as the Mount Everest of chemistry due to its remarkable chemical complexity (Jan. 8, page 12). As detailed, professor Kishi’s synthesis in the ’90s was in no doubt a tremendous accomplishment in assembling its structure, having a backbone of 115 carbon atoms! What was overlooked by the author was an equally important history that is sadly often downplayed in the chemical literature in favor of chemical synthesis, and that has to do with the discovery and characterization of the natural product itself; palytoxin in this case during the ’70s and early ’80s. That work was led by the late Richard E. Moore of the University of Hawaii, who reported its structure and stereochemistry in two [Journal of the American Chemical Society] articles in 1981 and 1982 (DOI: 10.1021/ja00399a093 and DOI: 10.1021/ja00377a064). That work was the culmination of over a decade of research of incredible ingenuity at a time when chromatography, NMR, and other modern conveniences that we take for granted today were nonexistent or in their infancy. Additional discovery work by professor Daisuke Uemura from Shizuoka University at the time amplified the structure of palytoxin and its derivatives (Tetrahedron Lett. 1981, DOI: 10.1016/S0040-4039(01)90551-9). It was this collection of discovery work that made it possible for Kishi and others to finally assign a chemical structure to the name and fascinating history of palytoxin.So let’s not forget about the incredible chemists who illuminate for us the chemical faces of nature’s molecules that continue to inspire us in many scientific disciplines.Bradley Moore (son of Richard E. Moore)La Jolla, Calif.William FenicalDel Mar, Calif. Corrections Jan. 29, page 10: In the science brief on a possible technique to search for extraterrestrial life, the pair of gases given as the atmospheric disequilibrium on Earth was incorrect. They should be methane and oxygen.Feb. 12, page 14: In a news story about NIGMS’s decision to stop funding a predoctoral fellowship, the number of fellowships should have been 85 since 2015, not per year. The NSF fellowships mentioned in the story are also available in the early years of graduate school, not just before students enter graduate school.Feb. 19, page 20: In the feature story on vaccines against drugs of abuse, the reference for the oxycodone vaccine entry in the table is incorrect. It is PLOS One 2014, DOI: 10.1371/journal.pone.0096547.

The Genealogical Tree of Ethanol: Gas-phase Formation of Glycolaldehyde, Acetic Acid, and Formic Acid

Abstract Despite the harsh conditions of the interstellar medium, chemistry thrives in it, especially in star-forming regions where several interstellar complex organic molecules (iCOMs) have been detected. Yet, how these species are synthesized is a mystery. The majority of current models claim that this happens on interstellar grain surfaces. Nevertheless, evidence is mounting that neutral gas-phase chemistry plays an important role. In this paper, we propose a new scheme for the gas-phase synthesis of glycolaldehyde, a species with a prebiotic potential and for which no gas-phase formation route was previously known. In the proposed scheme, the ancestor is ethanol and the glycolaldehyde sister species are acetic acid (another iCOM with unknown gas-phase formation routes) and formic acid. For the reactions of the new scheme with no available data, we have performed electronic structure and kinetics calculations deriving rate coefficients and branching ratios. Furthermore, after a careful review of the chemistry literature, we revised the available chemical networks, adding and correcting several reactions related to glycolaldehyde, acetic acid, and formic acid. The new chemical network has been used in an astrochemical model to predict the abundance of glycolaldehyde, acetic acid, and formic acid. The predicted abundance of glycolaldehyde depends on the ethanol abundance in the gas phase and is in excellent agreement with the measured one in hot corinos and shock sites. Our new model overpredicts the abundance of acetic acid and formic acid by about a factor of 10, which might imply a yet incomplete reaction network.