http://www.chemistrycentral.com/ The latest research articles published by Chemistry Central 2013-05-21T00:00:00Z Background: A molecule editor, i.e. a program facilitating graphical input and interactive editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. Today, when a web browser has become the universal scientific user interface, a tool to edit molecules directly within the web browser is essential. One of the most popular tools for molecular structure input on the web is the JME applet. Since its release nearly 15 years ago, however the web environment has changed and Java applets are facing increasing implementation hurdles due to their maintenance and support requirements, as well as security issues. This prompted us to update the JME editor and port it to a modern Internet programming language - JavaScript.SummaryThe actual molecule editing Java code of the JME editor was translated into JavaScript with help of the Google Web Toolkit compiler and a custom library that emulates a subset of the GUI features of the Java runtime environment. In this process, the editor was enhanced by additional functionalities including a substituent menu, copy/paste, drag and drop and undo/redo capabilities and an integrated help. In addition to desktop computers, the editor supports molecule editing on touch devices, including iPhone, iPad and Android phones and tablets. In analogy to JME the new editor is named JSME. This new molecule editor is compact, easy to use and easy to incorporate into web pages. Conclusions: A free molecule editor written in JavaScript was developed and is released under the terms of permissive BSD license. The editor is compatible with JME, has practically the same user interface as well as the web application programming interface. The JSME editor is available for download from the project web page http://peter-ertl.com/jsme/ http://www.jcheminf.com/content/5/1/24 Bruno Bienfait Peter Ertl Journal of Cheminformatics 2013, 5:24 2013-05-21T00:00:00Z ${item.identifier} /content/figures/1758-2946-5-24-toc.gif Journal of Cheminformatics 1758-2946 5 24 2013-05-21T00:00:00Z PDF Background: The novel chiral phosphorus-1,1-dithiolates [4-CH3OC6H4P(S)(OR)S-][H3N+C(CH3)3] were synthesized by the reaction of [RPS2)]2 (R = 4-MeOC6H4) or P2S5 and the respective alcohol ROH (R = myrtanyl, 2-naphthyl)ethyl, myrtenyl, borneol) in toluene. The reaction of phosphorus-1,1-dithiolates 1--4 and Au(tht)Cl, AuClPPh3 or AgNO3 and PPh3 gave rise to gold(I)- and silver(I)-complexes in THF. All compounds have been characterised by elemental analyses, IR, NMR (1H-, 13C- and 31P-) spectroscopy as well as MS measurements. Optical rotation values were confirmed the chirality of the compounds. The Compound 4 has been characterized structurally by X-ray crystallography. Results: Phosphorus-1,1,-dithiolate compounds were formed as liquids and were treated with suitable amine in order to convert them to their salts 1--4 . They have been successfully characterized spectroscopically (IR, 1H, 13C, 31P NMR) as well as mass spectra. The compound 4 has been also structurally by X-ray crystallography. The compound 4 crystallizes in the orthorhombic space group P2(1)2(1)2(1) with Z = 4. Compounds containing phosphorus and sulfur donor atoms are excellent ligands due to offering many metal complexes especially group 11--12 metals. The synthesis of gold(I) and silver(I) complexes with chiral phosphorus-1,1,-dithiolate and triphenylphosphine have been described and investigated. Conclusions: In the present work, we report the synthesis, charactreization of the chiral phosphorus-1,1-dithiolate ligands and preparing the gold(I) and silver(I) phosphorus-1,1-dithiolate or S-donor with phosphine complexes. The molecular structure of the Compound 4 was determined by X-ray diffraction. Due to an easy synthesis method of phosphorus-1,1-dithiolate compounds and a good complexion reagent, it is possible the improvement of the collecting metallic gold or silver from the minerals. When the more ionic salt of phosphorus-1,1-dithiolate compounds were prepared in this way, the water can be used as a cheap solvent. As a result, it can be an alternatively method for the collecting metallic gold or silver from the minerals in future. http://journal.chemistrycentral.com/content/7/1/89 Samet Solak Cemal Aydemir Mehmet Karakus Peter Lönnecke Chemistry Central Journal 2013, 7:89 2013-05-20T00:00:00Z ${item.identifier} /content/figures/1752-153X-7-89-toc.gif Chemistry Central Journal 1752-153X 7 89 2013-05-20T00:00:00Z PDF Background: A microclimate monitoring study was conducted in 2008 aimed at assessing the conservation risks affecting the valuable wall paintings decorating Ariadne's House (Pompeii, Italy). It was found that thermohygrometric conditions were very unfavorable for the conservation of frescoes. As a result, it was decided to implement corrective measures, and the transparent polycarbonate sheets covering three rooms (one of them delimited by four walls and the others composed of three walls) were replaced by opaque roofs. In order to examine the effectiveness of this measure, the same monitoring system comprised by 26 thermohygrometric probes was installed again in summer 2010. Data recorded in 2008 and 2010 were compared. Results: Microclimate conditions were also monitored in a control room with the same roof in both years. The average temperature in this room was lower in 2010, and it was decided to consider a time frame of 18 summer days with the same mean temperature in both years. In the rooms with three walls, the statistical analysis revealed that the diurnal maximum temperature decreased about 3.5 [degree sign]C due to the roof change, and the minimum temperature increased 0.5 [degree sign]C. As a result, the daily thermohygrometric variations resulted less pronounced in 2010, with a reduction of approximately 4 [degree sign]C, which is favorable for the preservation of mural paintings. In the room with four walls, the daily fluctuations also decreased about 4 [degree sign]C. Based on the results, other alternative actions are discussed aimed at improving the conservation conditions of wall paintings. Conclusions: The roof change has reduced the most unfavorable thermohygrometric conditions affecting the mural paintings, but additional actions should be adopted for a long term preservation of Pompeian frescoes. http://journal.chemistrycentral.com/content/7/1/87 Paloma Merello Fernando-Juan García-Diego Manuel Zarzo Chemistry Central Journal 2013, 7:87 2013-05-17T00:00:00Z 10.1186/1752-153X-7-87 /content/figures/1752-153X-7-87-toc.gif Chemistry Central Journal 1752-153X 7 87 2013-05-17T00:00:00Z PDF Background: Tremendous research from last twenty years has been pursued to cure human life against HIV virus. A large number of HIV protease inhibitors are in clinical trials but still it is an interesting target for researchers due to the viral ability to get mutated. Mutated viral strains led the drug ineffective but still used to increase the life span of HIV patients. Results: In the present work, 3D-QSAR and docking studies were performed on a series of Danuravir derivatives, the most potent HIV- protease inhibitor known so far. Combined study of 3D-QSAR was applied for Danuravir derivatives using ligand-based and receptor-based protocols and generated models were compared. The results were in good agreement with the experimental results. Additionally, docking analysis of most active 32 and least active 46 compounds into wild type and mutated protein structures further verified our results. The 3D-QSAR and docking results revealed that compound 32 bind efficiently to the wild and mutated protein whereas, sufficient interactions were lost in compound 46. Conclusion: The combination of two computational techniques would helped to make a clear decision that compound 32 with well inhibitory activity bind more efficiently within the binding pocket even in case of mutant virus whereas compound 46 lost its interactions on mutation and marked as least active compound of the series. This is all due to the presence or absence of substituents on core structure, evaluated by 3D-QSAR studies. This set of information could be used to design highly potent drug candidates for both wild and mutated form of viruses. http://journal.chemistrycentral.com/content/7/1/88 Zaheer Ul-Haq Saman Usmani Hina Shamshad Uzma Mahmood Sobia Halim Chemistry Central Journal 2013, 7:88 2013-05-17T00:00:00Z 10.1186/1752-153X-7-88 /content/figures/1752-153X-7-88-toc.gif Chemistry Central Journal 1752-153X 7 88 2013-05-17T00:00:00Z XML Background: Dufulin is a novel, highly effective antiviral agent that activatives systemic acquired resistance of plants. This compound is widely used in China to prevent and control viral diseases in tobacco, vegetable and rice. Dufulin can treat plants infected by the tobacco mosaic virus and the cucumber mosaic virus. However, the achiral analysis and residue determination of dufulin remain underdeveloped because of its high enantioselectivity rates and high control costs. The enantioselectivity of an antiviral compound is an important factor that should be considered when studying the effect of chiral pesticides on the environment. The enantioselective degradation of dufulin in water remains an important objective in pesticide science. Results: The configuration of dufulin enantiomers was determined in this study based on its circular dichroism spectra. The S-(+)-dufulin and R-(-)-dufulin enantiomers were separated and identified using an amylose tris-(3,5-dimethylphenylcarbamate) chiral column by normal phase high-performance liquid chromatography. The degradation of the rac-dufulin racemate and its separate enantiomers complied with first-order reaction kinetics and demonstrated acceptable linearity. The enantioselective photolysis of rac-dufulin allowed for the faster degradation of R-(-)-dufulin, as compared with S-(+)-dufulin. However, S-(+)-dufulin was hydrolyzed faster than its antipode. Conclusion: The photolysation and hydrolyzation of dufulin in water samples normally complied with the first-order kinetics and demonstrated acceptable linearity (R2>0.66). A preferential photolysation of the R-(-)-enantiomer was observed in water samples. Moreover, the S-(+)-enantiomer was hydrolyzed faster than its antipode. http://journal.chemistrycentral.com/content/7/1/86 Kankan Zhang Deyu Hu Huijun Zhu Jinchuan Yang Jian Wu Ming He Linhong Jin Song Yang Baoan Song Chemistry Central Journal 2013, 7:86 2013-05-16T00:00:00Z 10.1186/1752-153X-7-86 /content/figures/1752-153X-7-86-toc.gif Chemistry Central Journal 1752-153X 7 86 2013-05-16T00:00:00Z PDF Background: alpha-Mangostin was extracted with methanol from the rind of mangosteen fruit and purified by using silica gel column chromatography technique. The compound is characterised using infrared, 13C and 1H NMR as well as UV--vis spectroscopy. The alpha-mangostin dispersion in colloidal systems was studied by incorporating it with an ionic microgel, poly (N-Isopropylacrylamide)-co-2VP at different pH.ResultThe DLS result showed the size of microgel-alpha-mangostin mixture declined from 548 nm to 200 nm upon the increment of the pH. Moreover, it was found the morphology of loaded compound depended largely on the nature of the continuous phase of the microgel system. Interestingly, by manipulating the pH, alpha-mangostin tends to form crystal at extremely low pH and transforms into spherical shapes at pH 6. Conclusion: This research shows different structures of the alpha-mangostin particle that are attributed by adjusting the pH using microgel systems as a template. http://journal.chemistrycentral.com/content/7/1/85 Madihah Ahmad Bohari M Yamin Azwan Mat Lazim Chemistry Central Journal 2013, 7:85 2013-05-16T00:00:00Z 10.1186/1752-153X-7-85 /content/figures/1752-153X-7-85-toc.gif Chemistry Central Journal 1752-153X 7 85 2013-05-16T00:00:00Z PDF Background: This study investigated the oxidation of selected progestagenic steroid hormones by potassium permanganate at pH 6.0 and 8.0 in ultrapure water and wastewater effluents, using bench-scale assays. Second order rate constants for the reaction of potassium permanganate with progestagens (levonorgestrel, medroxyprogesterone, norethindrone and progesterone) was determined as a function of pH, presence of natural organic matter and temperature. This work also illustrates the advantages of using a novel analytical method, the laser diode thermal desorption (LDTD-APCI) interface coupled to tandem mass spectrometry apparatus, allowing for the quick determination of oxidation rate constants and increasing sample throughput. Results: The second-order rate constants for progestagens with permanganate determined in bench-scale experiments ranged from 23 to 368 M-1 sec-1 in both wastewater and ultrapure waters with pH values of 6.0 and 8.0. Two pairs of progestagens exhibited similar reaction rate constants, i.e. progesterone and medroxyprogesterone (23 to 80 M-1 sec-1 in ultrapure water and 26 to 149 M-1 sec-1 in wastewaters, at pH 6.0 and 8.0) and levonorgestrel and norethindrone (179 to 224 M-1 sec-1 in ultrapure water and 180 to 368 M-1 sec-1 in wastewaters, at pH 6.0 and 8.0). The presence of dissolved natural organic matter and the pH conditions improved the oxidation rate constants for progestagens with potassium permanganate only at alkaline pH. Reaction rates measured in Milli-Q water could therefore be used to provide conservative estimates for the oxidation rates of the four selected progestagens in wastewaters when exposed to potassium permanganate. The progestagen removal efficiencies was lower for progesterone and medroxyprogesterone (48 to 87 %) than for levonorgestrel and norethindrone (78 to 97 %) in Milli-Q and wastewaters at pH 6.0-8.2 using potassium permanganate dosages of 1 to 5 mg L-1 after contact times of 10 to 60 min. Conclusion: This work presents the first results on the permanganate-promoted oxidation of progestagens, as a function of pH, temperature as well as NOM. Progestagen concentrations used to determine rate constants were analyzed using an ultrafast laser diode thermal desorption interface coupled to tandem mass spectrometry for the analysis of water sample for progestagens. http://journal.chemistrycentral.com/content/7/1/84 Paul B Fayad Arash Zamyadi Romain Broseus Michèle Prévost Sébastien Sauvé Chemistry Central Journal 2013, 7:84 2013-05-15T00:00:00Z 10.1186/1752-153X-7-84 /content/figures/1752-153X-7-84-toc.gif Chemistry Central Journal 1752-153X 7 84 2013-05-15T00:00:00Z PDF Background Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others can link back using Uniform Resource Identifiers (URIs).RDF makes the data machine-readable and uses extensible vocabularies for additional information, making it easierto scale up inference and data analysis.Results This paper describes recent developments in an ongoing project converting data from the ChEMBL database into RDF triples.Relative to earlier versions, this updated version of ChEMBL-RDF uses recently introduced ontologies, including CHEMINF and CiTO;exposes more information from the database; and is now available as dereferencable, linked data.To demonstrate these new features, we present novel use cases showing further integration withother web resources, including Bio2RDF, Chem2Bio2RDF, and ChemSpider, and showing the use of standardontologies for querying.Conclusions We have illustrated the advantages of using open standards and ontologies to link the ChEMBL databaseto other databases. Using those links and the knowledge encoded in standards and ontologies, the ChEMBL-RDFresource creates a foundation for integrated semantic web cheminformatics applications,such as the presented decision support. http://www.jcheminf.com/content/5/1/23 Egon L Willighagen Andra Waagmeester Ola Spjuth Peter Ansell Antony J Williams Valery Tkachenko Janna Hastings Bin Chen David J Wild Journal of Cheminformatics 2013, 5:23 2013-05-08T00:00:00Z 10.1186/1758-2946-5-23 ChEMBL database as linked open data <p>An ongoing project converting data from the ChEMBL database into RDF triples. The ChEMBL-RDF resource creates a foundation for integrated semantic web cheminformatics applications.</p> /content/figures/1758-2946-5-23-toc.gif Journal of Cheminformatics 1758-2946 5 23 2013-05-08T00:00:00Z PDF Background: There are only limited publications devoted to the synthesis of especially thiazolo[3,2-a]quinazoline which involved reaction of 2-mercaptopropargyl quinazolin-4-one with various aryl iodides catalyzed by Pd-Cu or by condensation of 2-mercapto-4-oxoquinazoline with chloroacetic acid, inspite of this procedure was also reported in the literature to afford the thiazolo [2,3-b] quinazoline. So the multistep synthesis of the thiazolo [3,2-a] quinazoline suffered from some flaws and in this study we have synthesized a novel class of thiazoloquinazolines by a simple and convenient method involving catalysis by 1,4-diazabicyclo[2.2.2]octane (DABCO). Results: A new and convenient one-pot synthesis of a novel class of 2-arylidene-2H-thiazolo [3,2-a]quinazoline-1,5-diones 9a-i was established through the reaction between methyl-2-(2-thio- cyanatoacetamido)benzoate (4) and a variety of arylidene malononitriles 8a-i in the presence of DABCO as a mild and efficient catalytic system via a Michael type addition reaction and a mechanism for formation of the products observed is proposed. Moreover 4 was converted to ethyl-2-[(4-oxo-3,4-dihydroquinazolin-2-yl)thio]acetate (10) upon reflux in ethanol containing DABCO as catalyst. The latter was reacted with aromatic aldehydes and dimethylformamide dimethylacetal (DMF-DMA) to afford a mixture of two regioselectively products with identical percentage yield, these two products were identified as thiazolo[3,2-a]quinazoline 9,13 and thiazolo[2,3-b]quinazoline 11,12 derivatives respectively. The structure of the compounds prepared in this study was elucidated by different spectroscopic tools of analyses also the X-ray single crystal technique was employed in this study for structure elucidation, Z/E potential isomerism configuration determination and to determine the regioselectivity of the reactions. Conclusion: A simple and efficient one-pot synthesis of a novel class of 2-arylidene-2H-thiazolo[3,2-a]quinazoline-1,5-diones 9a-i was established through DABCO catalyzed Michael type addition reaction. In addition many fused quinazoline and quinazoline derivatives were synthesized which appeared as valuable precursors in synthetic and medicinal chemistry. http://journal.chemistrycentral.com/content/7/1/82 Haider Behbehani Hamada Mohamed Ibrahim Chemistry Central Journal 2013, 7:82 2013-05-07T00:00:00Z 10.1186/1752-153X-7-82 /content/figures/1752-153X-7-82-toc.gif Chemistry Central Journal 1752-153X 7 82 2013-05-07T00:00:00Z PDF Within recent years nucleic acids have become a focus of interestfor prototype implementations of molecular computingconcepts. During the same period the importance of ribonucleic acidsas components of the regulatory networks within living cells hasincreasingly been revealed. Molecular computers are attractive dueto their ability to function within a biological system; anapplication area extraneous to the present information technologyparadigm. The existence of natural information processingarchitectures (predominately exemplified by protein) demonstratesthat computing based on physical substrates that are radicallydifferent from silicon is feasible. Two key principles underliemolecular level information processing in organisms: conformationaldynamics of macromolecules and self-assembly of macromolecules.Nucleic acids support both principles, and moreover computationaldesign of these molecules is practicable. This study demonstratesthe simplicity with which one can construct a set of nucleic acidcomputing units using a new computational protocol. With the newprotocol, diverse classes of nucleic acids imitating the completeset of boolean logical operators were constructed. These nucleicacid classes display favourable thermodynamic properties and aresignificantly similar to the approximation of successful candidatesimplemented in the laboratory. This new protocol would enable theconstruction of a network of interconnecting nucleic acids (as acircuit) for molecular information processing. http://www.jcheminf.com/content/5/1/22 Effirul Ikhwan Ramlan Klaus-Peter Zauner Journal of Cheminformatics 2013, 5:22 2013-05-07T00:00:00Z 10.1186/1758-2946-5-22 /content/figures/1758-2946-5-22-toc.gif Journal of Cheminformatics 1758-2946 5 22 2013-05-07T00:00:00Z PDF