FACILE FACILE A0 PDF
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We demonstrate that using our readily extensible specification, it is possible to efficiently integrate multiple disparate chemical data sources, while retaining appropriate correspondence of chemical descriptors, with very little additional effort. We demonstrate the impact of some of our representational decisions on the performance of chemically-aware knowledgebase searching and rudimentary reaction candidate selection.
Finally, we provide access to the tools necessary to carry out chemical entity encoding in CHESS, along with a sample knowledgebase.
Conclusions By harnessing the power of Semantic Web technologies with CHESS, it is possible to provide a means of facile cross-domain chemical knowledge integration with full preservation of data correspondence and provenance. Our representation builds on existing cheminformatics technologies and, by the virtue of RDF specification, remains flexible and amenable to application- and domain-specific annotations without compromising chemical data integration.
We conclude that the adoption of a consistent and semantically-enabled chemical specification is imperative for surviving the coming chemical data deluge and supporting systems science research. Background The importance of cataloguing and adequately representing chemical information has been realized fairly early in the development of chemistry and related sciences. From the dawn of the era of organic synthesis, thousands of chemical entities, reactions, and experimental outcomes were catalogued and stored in a human-readable form, some dating to as early as the eighteenth century when the understanding of molecular reactivity and chemical structure was nowhere near its current level preserved in e.
During the relatively long history of the development of chemical information archiving technologies, a large number of persistent redundancies and factors complicating chemical knowledge federation have been introduced.
It may be argued, however, that these problems may be reduced to three major categories, some of which have been only recently partially addressed: i a lack of a consensus canonical identifiers of all chemical entities, including reactions and macromolecules, as well as and their constituents, ii absence of a single common flexible representation to satisfy the needs of most sub-disciplines of chemistry, and iii a lack of a consensus chemical database structure or schema.
We argue that the bulk of present-day complications in integrating chemical information can be traced to these three problems and that until an information representation that addresses these issues is introduced, truly integrative chemical research shall be a complicated and costly endeavour. Consensus Chemical Entity Identifiers Many modern chemical databases rely on internal chemical entity identifiers which are usually created in a sequential manner, producing an index whose value increases for every new chemical entity in the database [ 2 - 5 ].
Unfortunately, such indexing systems require manual or semi-automated cross-database matching, resulting in difficulties of federating chemical data. Attempts to create reproducible and canonical molecular identifiers that bear molecular graph information could be dated to the introduction of computers to the field of chemistry in the 20th century. The fact that molecules could be represented as graphs and features of these graphs could be used to arrive at a shorthand depiction of molecular structure, had swiftly led to the creation of the first fragment-based line notation in chemistry: the Wiswesser Line Notation WLN [ 6 ].
In this notation, molecular fragments were abbreviated and recorded with a limited character set to reconstitute various molecular parts and their connectivity. Unfortunately, no efficient way to create a canonical molecular representation for this line notation existed, meaning that a given molecule could be referred to by multiple different WLN strings in different chemical databases.
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This shortcoming was overcome with the introduction of the SMILES notation [ 7 ], which explicitly represented chemical molecules as graphs with atoms being nodes and bonds edges, along with an efficient algorithm to create a canonical, reproducible SMILES string representation of a given molecule. Finally, The International Chemical Identifier InChI notation has addressed this issue by providing algorithms and software to enable consistent canonical representation of chemical structures, but has unfortunately not yet addressed the efficient canonical representation of many other chemical entities, such as reactions and macromolecules [ 8 ].
More recently, due to the unwieldy nature of InChI for many larger molecules as well as web search engine complications, InChI keys have been introduced, producing a character hash based on the elements of chemical graph structure [ 8 ]. Although InChI keys cannot be used to reconstitute chemical structure without lookup tables, their use has enabled cross-database chemical searches using common web search engines.
It is not unreasonable to believe that a universal adoption of the IUPAC standard InChI keys in the role of database indexes could potentially facilitate knowledge federation immensely. Common Chemical Information Representation Simple line notations have been useful as chemical structure identifiers and bearers of information necessary for the vast majority of cheminformatics tasks, such as chemical database searching or basic reactive transformation outcome predictions.
A Facile Synthetic Route to Ether Diols Derived from 1,1
HNO3 is another necessary ingredient in this synthetic system. CPyCl plays a crucial role in the structure formation of mesoporous silica with Ia3d cubic.
Results and discussion H. Wang et al. Phenol, as a polar organic additive reducing the repulsive interaction of hydrophilic groups, results in the decrease of a0; and it inserts into the micelle palisade  to increase the value of V. The decrease of a0 and the increase of V induce to the increase in the g value.
This is the reason why absence of phenol relates to formation of hexagonal p6mm mesoporous silica with a small g value. The same reason can explain why excess phenol causes the appearance of mesoporous silica with lamellar structure with a large g value. HNO3 is another influencing element of g value.
In the surfactant solution the anions are more or less hydrated. More strongly hydrated ions have, in general, bigger ionic radii and bind less closely and strongly on the head group of the surfactant. The small anions contribute to the partial reduction in the electrostatic repulsion between the charged surfactant head groups and the decrease in the effective head group area of surfactant a0, therefore resulting in a significant increase in the g value .
Consequently HNO3 leads to the formation of the Ia3d cubic mesophase with a large g value and HCl or H2SO4 favors the formation of the hexagonal p6mm mesophase with a small g value. CTAB is commonly used as template in acid condition to direct the formation of hexagonal p6mm mesoporous silica. However CPyCl has a large hexahydric ring that can be folded in the surfactant tail region to enlarge the value of V, therefore the g value is enlarged.
Since CPyCl, phenol and HNO3 all have the character to increase the g value, mesoporous silica with Ia3d cubic symmetry can thus be synthesized in acidic condition at room temperature. Conclusions Mesoporous silica with Ia3d cubic symmetry is synthesized in a facile way by using CPyCl as template, phenol as organic additive and HNO3 as the acid catalyst at room temperature.
Index of /~mackerle/dl/temp/italstina/Facile
These conditions are relatively mild and easy to be controlled, and the resulting samples possess a larger surface area than the MCM synthesized with CTAB template under alkaline conditions. References  J. Xu, Z. Luan, Y. He, W. Zhou, L. Kevan, Chem. Zhang, Y.
Meng, D. Gu, Y. Yan, C. Yu, B. Tu, D. Zhao, J. Liu, A.
Karkamkar, T. Pinnavaia, Chem. Chen, L.
Huang, Q. Li, Chem. Liu, B.
Tian, C. Yu, F. Gao, S. Xie, B.In all cases, we observed either memory exhaustion despite having allocated 5GB of memory , or premature termination.
We conclude that the adoption of a consistent and semantically-enabled chemical specification is imperative for surviving the coming chemical data deluge and supporting systems science research. Furthermore, we believe that, within the limit of providing an expressive enough specification of chemical entities under investigation, the efficiency of querying a knowledgebase created using a given knowledge representation is a good indicator of the efficiency of the representation itself.
Elon Musk: Ultrasound promoted synthesis of a,a0 -bis substituted furfurylidene cycloalkanones and chalcones. J Chem Inf Comput Sci. Improved micro- wave-induced synthesis of chalcones and related enones.