IUPAC Name Research Articles

How to specify the structure of substituted blade-like zigzag diamondoids

Abstract Abstract The dualist of an [n]diamondoid consists of vertices situated in the centers of each of the n adamantane units, and of edges connecting vertices corresponding to units sharing a chair-shaped hexagon of carbon atoms. Since the polycyclic structure of diamondoids is rather complex, so is their nomenclature. For specifying chemical constitution or isomerism of all diamondoids the Balaban-Schleyer graph-theoretical approach based on dualists has been generally adopted. However, when one needs to indicate the location of C and H atoms or of a substituent in a diamondoid or the stereochemical relationships between substituents, only the IUPAC polycycle nomenclature (von Baeyer nomenclature) provides the unique solution. This is so since each IUPAC name is associated with a unique atom numbering scheme. Diamondoids are classified into catamantanes (which can be regular or irregular), perimantanes, and coronamantanes. Regular catamantanes have molecular formulas C4n+6H4n+12. Among regular catamantanes, the rigid blade-shaped zigzag catamantanes (so called because their dualists consist of a zigzag line with a code of alternating digits 1 and 2) exhibit a simple pattern in their von Baeyer nomenclature. Their carbon atoms form a main ring with 4n + 4 atoms, and the remaining atoms form two 1-carbon bridges. All zigzag [n]catamantanes with n > 2 have quaternary carbon atoms, and the first bridgehead in the main ring is such an atom. Their partitioned formula is Cn−2(CH)2n+4(CH2)n+4. As a function of their parity, IUPAC names based on the von Baeyer approach have been devised for all zigzag catamantanes, allowing the unique location for every C and H atom. The dualist of such a zigzag catamantane defines a plane bisecting the molecule, and the stereochemical features of hydrogens attached to secondary carbon atoms can be specified relatively to that plane. Graphical abstract

Corrosion inhibition and adsorption properties of pharmaceutically active compound esomeprazole on mild steel in hydrochloric acid solution

The effect of a pharmaceutically active compound esomeprazole (IUPAC name: [S]-5-methoxy-2-[(4-methoxy-3,5-dimethylpyridin-2-yl)methylsulfinyl]-3H-benzoimidazole) on the corrosion of mild steel in 0.5 M HCl solution has been investigated using weight loss, potentiodynamic polarization, electrochemical impedance spectroscopy, adsorption isotherm, and scanning electron microscope (SEM). Inhibition efficiencies of esomeprazole increased as the concentration of esomeprazole increases, but decreased with increases in temperature, immersion period, and acid concentration. The inhibition was assumed to occur via adsorption of the inhibitor molecule on the metal surface. The Langmuir adsorption isotherm was found to be the best isotherm that described the adsorption characteristics of the inhibitor. Also, the activation and thermodynamic parameters of dissolution and adsorption were calculated and discussed. Further, the SEM analysis confirms the formation of an adsorbed protective film on the mild steel surface. Based on all these results, esomeprazole is found to inhibit the corrosion of mild steel in 0.5 M HCl solution, and a plausible mechanism of corrosion inhibition is proposed.

SAM-e AND ITS THERAPEUTIC PRINCIPLES

S-Adenosylmethionine (SAM-e) which is an well-known super nutrient in countries like Europe , Italy, but unfortunately it is unknown in many countries, which is mainly available as nutrient supplement, same though it is not a completely new compound but can be found in our tissues performing trans methylation reaction(methyl donor) with  Iupac name as  [(3S)-3-amino-3-carboxypropyl]({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl})methylsulfanium .SAM-e stands first among all other drugs in treating depression, cirrhosis, osteoarthritis, Alzheimer disease, Though it was discovered in 1952 it self but it does not came in to lime light, much more studies are to be conducted to evaluate it uses and even the way it works can be inspiring to us in preparing its derivatives. Alcoholic cirrhosis patients when given SAM-e miraculously cured just by increasing the regeneration efficacy of the liver, this article mainly discuss the uses of SAMe and the principle mechanism involved in it.

A pharmaceutical product as corrosion inhibitor for carbon steel in acidic environments

A pharmaceutical product, Trimethoprim (TMP), IUPAC name: 5-(3,4,5-trimethoxybenzyl)pyrimidine-2,4-diamine was investigated, as inhibitor to prevent carbon steel corrosion in acidic environments. The study was performed using weight loss and electrochemical measurements, in temperatures ranging between 25–55°C. The surface morphology before and after corrosion of carbon steel in 1.0 M HCl solution in the presence and absence of TMP was evaluated using scanning electron microscopy (SEM). The inhibition efficiency (IE) increased with the increasing of the inhibitor concentration, reaching a maximum value of 92% at 25°C and 0.9 mM TMP, and decreased with increasing temperature. The inhibition of carbon steel corrosion by TMP can be attributed to the adsorption ability of inhibitor molecules onto the reactive sites of the metal surface. The adsorption is spontaneous and it is best described by the Langmuir isotherm. The apparent activation energy (Ea) for the corrosion process in the absence and presence of TMP was evaluated from Arrhenius equation, to elucidate its inhibitive properties.

The effect of redox conditions on sphagnum acid thermochemolysis product distributions in a northern peatland

Thermally assisted hydrolysis and methylation (THM) in the presence of tetramethylammonium hydroxide (TMAH) of a range of layers in eight peat cores from the Ryggmossen peatland (central Sweden) was carried out. This yielded a complex mixture including components I (methylated 4-isopropenylphenol (IUPAC name: 1-methoxy-4-(prop-1-en-2-yl)benzene)), IIa/b (methylated cis/trans 3-(4′-hydroxyphen-1-yl)but-2-enoic acid (IUPAC names: (E/Z)-methyl 3-(4-methoxyphenyl)but-2-enoate)) and III (methylated 3-(4′-hydroxyphen-1-yl)but-3-enoic acid (IUPAC name: methyl 3-(4-methoxyphenyl)but-3-enoate)) which have been assigned as products from “bound” sphagnum acid. The proportion of the individual sphagnum acid products relative to total Sphagnum yield revealed the simultaneous degradation of all four components in the unsaturated layer (which is characterised by oxic conditions) concomitant with the decrease of the total Sphagnum yield. Following their degradation in the surficial oxic layer, the total amounts of the sphagnum acid thermochemolysis products stabilise in the deeper seasonally saturated peat. With a further increase in burial depth, in the permanently saturated anoxic peat, the distribution of thermochemolysis products becomes dominated by I. The increase of σI% relative to σ(IIa/b and III)% indicates that the mode of binding of sphagnum acid into the peat changes as a function of burial depth and hence position relative to the water table. Therefore the relative amounts of the four sphagnum acid THM products show some promise as indicators of redox conditions in young surficial peats.

Analyzing the solubility of fluoxetine hydrochloride in supercritical carbon dioxide

In the pharmaceutical industry where the supercritical fluid-based technologies are utilized it is very important and vital to know the accurate value of the equilibrium solubility of solids required for the engineers to determine the size of the equipments. According to this requirement, the purpose of this study was measuring the solubility of fluoxetine hydrochloride with IUPAC name of 3-phenyl-3-[4-(trifluoromethyl)phenoxy]propan-1-amine hydrochloride using a static method coupled with gravimetric method. The measured solubility data at the temperature and pressure range of 308.15–338.15K and 16–40MPa was ranged between 2.65×10−5 and 8.12×10−4 based on the mole fraction. The results revealed that the solubility was increased when the pressure was increased while the effect of the temperature was more complex. Finally, the measured solubility data were correlated using three different correlations namely Bartle et al., Mendez-Santiago–Teja and Kumar and Johnston. The results of modeling revealed that the Bartle et al. model leads to the lowest average absolute relative deviation (AARD %) of 9.48.

Design of optimal solvent for extraction of bio–active ingredients from six varieties of Medicago sativa

BackgroundExtensive research has been performed worldwide and important evidences were collected to show the immense potential of plants used in various traditional therapeutic systems. The aim of this work is to investigate the different extracting solvents in terms of the influence of their polarity on the extracting ability of bioactive molecules (phenolic compounds) from the M. sativa flowers.ResultsThe total phenolic content of samples was determined using the Folin Ciocalteu (FC) procedure and their antioxidant activity was assayed through in vitro radical decomposing activity using the radical DPPH° assay (IUPAC name for DPPH is (phenyl)–(2,4,6–trinitrophenyl) iminoazanium). The results showed that water was better than methanol and acetic acid for extracting bioactive compounds, in particular for total phenolic compounds from the flowers of alfalfa. The average content of bioactive molecules in methanol extract was 263.5±1.02 mg GAE/100g of dry weight lyophilized extract. The total phenolic content of the tested plant extracts was highly correlated with the radical decomposing activity. However, all extracts were free–radical inhibitors, but the water extract was more potent than the acetic and the methanol ones. The order of inhibitor effectiveness (expressed by IC50) proved to be: water extract (0.924mg/mL) > acetic acid extract (0.154mg/mL) > methanol (0.079mg/mL). The profiles of each extract (fingerprint) were characterized by FT–MIR spectroscopy.ConclusionsThe present study compares the fingerprint of different extracts of the M. sativa flowers, collected from the wild flora of Romania. The total phenolic content of the tested plant extracts was highly correlated with the radical decomposing activity. The dependence of the extract composition on the solvent polarity (acetic acid vs. methanol vs. water) was revealed by UV–VIS spectrometry and Infrared fingerprint.

Gold-nanoparticle Inks for Room-temperature Formation of Conductive Films

Abstract We show that aqueous inks containing Au nanocrystals that were slightly modified with mercaptosuccinic acid (MSA, IUPAC name: sulfanylsuccinic acid) turn into conductive films after being cured in room-temperature air. Because of the highly hydrophilic nature of MSA, the nanoparticles maintain good dispersion in water. The conductive film exhibits an electrical resistivity in the order of 10−5 Ω cm, and its temperature coefficient in the range from 290 to 20 K was 7 × 10−5 K−1 without any post-treatments such as annealing, light irradiation, or solution-immersing processes.

Crystal Structures, Reaction Rates, and Selected Physical Properties of Halo-Boronsubphthalocyanines (Halo = Fluoride, Chloride, and Bromide)

The physical properties, including the solid state arrangement, photophysics, solubility, and electrochemical behavior of a series of halo-BsubPcs (halo = F, Cl, Br) have been measured (IUPAC name halo-(7,12:14,19-diimino-21,5-nitrilo-5H-tribenzo(c,h,m)(1,6,11)triazacyclopentadecinato)-boron(III)). We have found that across the series all are relatively similar in most regards. Exceptions include that F-BsubPc can be 5 to 25 times more soluble than Cl-BsubPc in common organic solvents. F-BsubPc was also found to be hydrolytically stable under the conditions tested, whereas Cl-BsubPc and Br-BsubPc readily hydrolyzed to form HO-BsubPc. The relative rates of reaction for the series of halo-BsubPcs under standard phenoxylation conditions have also been measured. It was found that F-BsubPc does not undergo phenoxylation, whereas Br-BsubPc showed a markedly higher reaction rate relative to Cl-BsubPc. Based on these data some assumptions can be made as to the suitability of either F-BsubPc or Br-BsubPc to be use...

A novel lariat-silacrown ether based in sol–gel process: synthesis, characterization and interaction study with the copper(II) ion

The synthesis and characterization of the lariat-silacrown ether (Sila15NH—IUPAC name: 3-[1-[[1-(3-aminopropyl)-2,5,8,11,14-pentaoxa-1-silacyclotetradec-1-yl] oxy]-2,5,8,11,14-pentaoxa-1-silacyclotetradec-1-yl]propan-1-amine) and its complex with copper(II) ion, Cu(II)–Sila15NH, are reported in this work. Tetraethylene glycol, 3-aminopropyl triethoxysilane and metallic sodium were employed as precursors and the lariat-silacrown ether obtained in a good yield (64 %) was characterized by elemental analysis, infrared spectroscopy (FTIR) and nuclear magnetic resonance of 1H, 13C and 29Si. The Cu(II)–Sila15NH was characterized by elemental analysis and FTIR. The straightforward Cu(II) complex formation suggests this property could be explored for analytical purposes.

Building an R&D chemical registration system

Small molecule chemistry is of central importance to a number of R&D companies in diverse areas such as the pharmaceutical, nutraceutical, food flavoring, and cosmeceutical industries. In order to store and manage thousands of chemical compounds in such an environment, we have built a state-of-the-art master chemical database with unique structure identifiers. Here, we present the concept and methodology we used to build the system that we call the Unique Compound Database (UCD). In the UCD, each molecule is registered only once (uniqueness), structures with alternative representations are entered in a uniform way (normalization), and the chemical structure drawings are recognizable to chemists and to a cartridge. In brief, structural molecules are entered as neutral entities which can be associated with a salt. The salts are listed in a dictionary and bound to the molecule with the appropriate stoichiometric coefficient in an entity called “substance”. The substances are associated with batches. Once a molecule is registered, some properties (e.g., ADMET prediction, IUPAC name, chemical properties) are calculated automatically. The UCD has both automated and manual data controls. Moreover, the UCD concept enables the management of user errors in the structure entry by reassigning or archiving the batches. It also allows updating of the records to include newly discovered properties of individual structures. As our research spans a wide variety of scientific fields, the database enables registration of mixtures of compounds, enantiomers, tautomers, and compounds with unknown stereochemistries.

Thermodynamic properties of 9-fluorenone: Mutual validation of experimental and computational results

Measurements leading to the calculation of thermodynamic properties for 9-fluorenone (IUPAC name 9H-fluoren-9-one and Chemical Abstracts registry number [486-25-9]) in the ideal-gas state are reported. Experimental methods were adiabatic heat-capacity calorimetry, inclined-piston manometry, comparative ebulliometry, and combustion calorimetry. Critical properties were estimated. Molar entropies for the ideal-gas state were derived from the experimental studies at selected temperatures T between T=298.15K and T=600K, and independent statistical calculations were performed based on molecular geometry optimization and vibrational frequencies calculated at the B3LYP/6−31+G(d,p) level of theory. Values derived with the independent methods are shown to be in excellent accord with a scaling factor of 0.975 applied to the calculated frequencies. This same scaling factor was successfully applied in the analysis of results for other polycyclic molecules, as described in recent articles by this research group. All experimental results are compared with property values reported in the literature. Thermodynamic consistency between properties is used to show that several studies in the literature are erroneous.

Solubility of sulindac in the supercritical carbon dioxide: Experimental and modeling approach

Solubility measurements of solids in supercritical fluids have been increasingly performed during the past three decades, and semi-empirical models are utilizing as one of the best methods to fit this type of data. For the proper design of supercritical fluid drug process, it is essential to have a sufficient knowledge of the drug solubilities in supercritical fluids particularly carbon dioxide because of its green characterization. In this regards, the solubility of sulindac with IUPAC name of {(1Z)-5-fluoro-2-methyl-1-[4-(methylsulfinyl)benzylidene]-1H-indene-3-yl}acetic acid were examined in the wide ranges of temperature and pressure of 308.15–338.15 K and 160–400 bar, respectively, in supercritical carbon dioxide. The obtained results show the sulindac solubility was in the range of 3.65 × 10−5 to 8.69 × 10−3 mole fraction and additionally was correlated with four density based semi-empirical correlations namely, Mendez-Santiago–Teja, Bartle, Chrastile and Kumar and Johnston methods.

Study of the corrosion products formed on carbon steel surface in hydrochloric acid solution

Effect of an antibacterial drug, sulfacetamide, IUPAC name N-[(4-aminophenyl) sulfonyl] acetamide (APSA), on the corrosion products formed on carbon steel surface in 1.0 mol L−1 HCl solution has been investigated using mass loss, X-ray photoelectron spectroscopy (XPS), and simultaneous thermal and differential scanning calorimetry/differential thermal analysis (TG/DSC/DTA). Mass loss measurements reveal that the corrosion rate of carbon steel is retarded by APSA and that the inhibition efficiency of this inhibitor increases with increasing the concentration. XPS analysis shows that, at this stage, the main product of corrosion is a non-stoichiometric Fe3+ oxyhydroxide, consisting of a mixture of FeO(OH) in anhydrous or hydrated forms, containing Cl− inclusions and adsorbed APSA molecules. The mechanism of inhibition was discussed in light of the chemical structure of the investigated inhibitor. The corrosion products were analyzed using TG/DSC/DTA technique.

Making SharePoint® Chemically Aware™

BackgroundThe use of SharePoint® collaboration software for content management has become a critical part of today's drug discovery process. SharePoint 2010 software has laid a foundation which enables researchers to collaborate and search on various contents. The amount of data generated during a transition of a single compound from preclinical discovery to commercialization can easily range in terabytes, thus there is a greater demand of a chemically aware search algorithm that supplements SharePoint which enables researchers to query for information in a more intuitive and effective way. Thus by supplementing SharePoint with Chemically Aware™ features provides a great value to the pharmaceutical and biotech companies and makes drug discovery more efficient. Using several tools we have integrated SharePoint with chemical, compound, and reaction databases, thereby improving the traditional search engine capability and enhancing the user experience.ResultsThis paper describes the implementation of a Chemically Aware™ system to supplement SharePoint. A Chemically Aware SharePoint (CASP) allows users to tag documents by drawing a structure and associating it with the related content. It also allows the user to search SharePoint software content and internal/external databases by carrying out substructure, similarity, SMILES, and IUPAC name searches. Building on traditional search, CASP takes SharePoint one step further by providing a intuitive GUI to the researchers to base their search on their knowledge of chemistry than textual search. CASP also provides a way to integrate with other systems, for example a researcher can perform a sub-structure search on pdf documents with embedded molecular entities.ConclusionA Chemically Aware™ system supplementing SharePoint is a step towards making drug discovery process more efficient and also helps researchers to search for information in a more intuitive way. It also helps the researchers to find information which was once difficult to find by allowing one to tag documents with molecular entities and integrating with image recognition software to find information from pdf documents.

J053022 混合気中の炭化水素燃料のダイナミクスの分子動力学的解析

Octane number of commercial gasoline as fuel for Otto cycle engine is defined by the mixture ratio of isooctane (IUPAC name: 2,2,4-trimethylpentane) of which octane number is 100 and n-heptane of which octane number is 0. In present study, molecular dynamics simulation of air-fuel mixture of isooctane or n-heptane is performed under various temperature and compression ratio conditions. Four kinds of kinetic energy of each chemical spices are analyzed. Total, translational, rotational and internal vibrational energies are defined and computed. Especially, definition of rotationalkinetic energy for a molecule as non-rigid system is examined in detail. Simulated results are inconsistent with the principle of equipartition for kinetic energy.

New sesquiterpene coumarin from the roots of Ferula latisecta.

The genus of Ferula belongs to the tribe Peucedaneae, subfamily of Apioideae and family of Umbelliferae with 133 species distributed throughout the Mediterranean area and central Asia, especially in the former USSR and neighboring countries such as Iran. The popular Persian name of the most of these species is "Koma". In this research we tried to isolate and elucidate the structure of new sesquiterpene in the root of Ferula latisecta (F. latisecta). Dried and powdered roots of F. latisecta were extracted with CH2Cl2 using a Soxhlet apparatus. The extract was concentrated in vacuo to give a red extract. The extract was subjected to column chromatography on silica gel. (1)H NMR, (13)C NMR, DEPT, (1)H-(1)H COSY, HMBC, HSQC, and NOESY spectra were the methods we used to elucidate the structure of new sesquiterpene in this plant. One new sesquieterpene coumarin, namely Latisectin and IUPAC name [1-(2-Hydroxy-4-methoxy-phenyl)-3,4,8,12-tetramethyl-trideca-4,7,11-trien-1-one ] , together with one known compound , Kopetdaghin C, were isolated from the root of F. latisecta. In this research the structure of one new and one known sesquiterpene in the root of F. latisecta was elucidated.

Surface Analysis of Inhibitor Film Formed by 4-Amino-N-(1,3-thiazol-2-yl) Benzene Sulfonamide on Carbon Steel Surface in Acidic Media

ABSTRACT Inhibitive properties of the antibacterial sulfa drug sulfathiazole—IUPAC name being 4-amino-N-(1,3-thiazol-2-yl) benzene sulfonamide—on the corrosion of carbon steel in 1.0 M HCl solution were investigated using weight loss measurements, electrochemical impedance spectroscopy (EIS), scanning electron microscopy (SEM), and X-ray photoelectron spectroscopy (XPS). Sulfathiazole is a good adsorption inhibitor, and the inhibition efficiency increases with increasing concentration. Adsorption is spontaneous and is best described by Temkin isotherm. XPS analysis showed, at this stage, that the main product of corrosion is a nonstoichiometric Fe3+ oxide/oxyhydroxide consisting of a mixture of Fe2O3, α, and γ-FeO(OH) and/or Fe(OH)3, where α, γ-FeO(OH) is the main phase.

T.S.S. Dikshith: Handbook of Chemicals and Safety

Every year about 400 million tonnes of chemicals in 100,000 varieties are manufactured globally. Every year about 1,000 new variations are added. It is suggested that most have never been tested for their effects on health and the environment. Furthermore, it is claimed that the majority of the newly released additions are accepted without any tests or regulation, and the aberrations caused by these chemicals go unnoticed. This sweeping statement would be rejected by many manufacturers, especially those in the pharmaceutical industry. Rightly or wrongly, very major incidents occur at remarkably regular frequency around the world: the London Smog (UK, 1952); Love Canal (USA, 1953); Seveso (Italy, 1976); Bhopal (India, 1984); Chernobyl (Ukraine, 1986); Exxon Valdez (USA, 1989); Donana (Spain, 1998); and Fukushima (Japan 2011). The very variation of the causes of these catastrophes exemplifies the extraordinary difficulty of defining what chemical contamination consists of, and what precautions can be used to prevent it. The adverse health effects and resulting fatalities caused by environmental pollution and chemical disasters are many. These are not necessarily limited to toxicity, the duration of exposure, and the individual’s age or health. There are many causes; and not all effects can be reduced or guarded against, demonstrated by the examples above. Would any nuclear designer of 35 years ago have been able to predict the 15-m tsunami that hit the Fukushima plant? The author states the intention of this book is to provide guidance to students, toxicologists, hygienists, basic chemists, engineers and occupational workers with a standardised and ready-reference source of data. The potential readership is then stretched further, by suggesting semi-skilled workers and householders would find it a useful ready-reference source. With these objectives in mind the text is clearly laid out, containing information about the use and possible health effects, immediate and long term effects, and hazards of chemical substances, all to be encountered when handling any of the chemicals listed. The listings also include correct identification, use and handling, separation when stored, and waste disposal. Some 50% of the contents are a compilation of chemical substances, listed alphabetically, and also by classification. Each individual chemical is compiled with its CAS number, IUPAC name, molecular formula, synonyms, trade names, use and exposure, toxicity and health effects, carcinogenicity, exposure limits, methods of storage, precautions, waste disposal and any relevant references. In supporting the recently introduced Globally Harmonised System of Classification and Labelling of Chemicals (GHS), the author is hopeful it will have a significant effect on reducing major disasters. Whilst a forward step, it seems equally likely that however much knowledge is available and however well it is applied, such events will keep occurring. Although most data given are available in many other sources, the presentation is concise, clear, quickly referenced and easily read—but it will only have appeal to those working in uncomplicated environments needing a quick reference source. Bibliography Handbook of Chemicals and Safety T.S.S. Dikshith CRC Press, Boca Raton, FL, USA, 2010, pp 531 ISBN 978-1-4398-2060-5 GBP 95.00, USD 149.95

Site-Directed Methyl Group Labeling as an NMR Probe of Structure and Dynamics in Supramolecular Protein Systems: Applications to the Proteasome and to the ClpP Protease

Methyl groups are powerful reporters of structure, motion, and function in NMR studies of supramolecular protein assemblies. Their utility can be hindered, however, by spectral overlap, difficulties with assignment or lack of probes in biologically important regions of the molecule studied. Here we show that (13)CH(3)-S- labeling of Cys side chains using (13)C-methyl-methanethiosulfonate ((13)C-MMTS) (IUPAC name: methylsulfonylsulfanylmethane) provides a convenient probe of molecular structure and dynamics. The methodology is demonstrated with an application focusing on the gating residues of the Thermoplasma acidophilum proteasome, where it is shown that the (13)CH(3)-S- label reports faithfully on the conformational heterogeneity and dynamics in this region of the complex. A second and related application involves labeling with (13)C-MMTS at the N-termini of the subunits comprising the E. coli ClpP protease that reveals multiple conformations of gating residues in this complex as well. These N-terminal residues adopt a single conformation upon gate opening.