About The ChemSpider Journal of Chemistry
The ChemSpider Journal of Chemistry is an experiment. We intend to demonstrate
how modern web technologies can be used to dramatically enhance the type of information
that can be communicated using web-based tools over standard online publishing approaches.
We are committed to hosting chemistry-related materials including synthesis, analytical
chemistry, solid state chemistry, chemical biology, cheminformatics, and molecular
modeling. The ChemSpider Journal of Chemistry publishes original research, review
articles, commentaries, methodologies, blog pages, book and software reviews. All
papers published in the ChemSpider Journal of Chemistry are made freely accessible
online immediately upon publication. We used a mixed review process of peer and
public review. For more information, please see the instructions for authors.
Editor-in-chief: Antony J. Williams, Royal Society of Chemistry, Thomas Graham House, Cambridge, UK
Editorial board
For further information and for all enquiries about the journal, please contact
the editor-in-chief at antony.williams-at-chemspider-dot-com.
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Colour prediction with JSpecView
Robert J. Lancashire and Craig A.D. Walters
Published:10/03/2010 10:58:45
A routine for the prediction of colour from visible spectra was developed for JSpecView. This involved curve fitting standard colour matching functions (CMF) as well as standard illuminant (D65) data so that visible spectral information, recorded between at least 400 and 700 nm, could be viewed and a prediction made of the colour.
A maximum of four structures are shown for information purposes
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 Abstract
 Thumbnails
 Structures
 Full Text
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Applications of Computer-Aided Methods of Structure Elucidation to the Revision of Chemical Structures. I. Structure Revision of Lamellarin g.
M. E. Elyashberg+, K. A. Blinov+, S.G. Molodtsov+, T.S. Churanova+, A.J. Williams.
Published:18/03/2009 11:20:33
The structure elucidation of new organic compounds is clearly one of the most common challenges for organic chemistry and the application of spectroscopy. Molecular structures are usually established on the basis of the combined treatment of data obtained from MS, NMR, IR and UV spectra. Among the various spectroscopic methods 2D NMR spectroscopy now plays an outstanding role in the process of structure determination and is a rich source of structural information. This information however is fuzzy by nature and different researchers can interpret the data in different ways. As a result, it is quite common that structures published in the literature by one group of researchers can be revised by another group. It can be expected that the number of incorrectly identified structures may be reduced if Computer Assisted Structure Elucidation systems (CASE) are used for the purpose of structure elucidation. To familiarize the chemistry community with the advantages of the methodology underpinning CASE systems we will present a series of articles in this journal where we shall try to show the readers how the application of an expert system can prevent a scientist from arriving at an incorrect structural solution and can reduce the time and effort necessary to elucidate a new organic compound. Our expert system Structure Elucidator will be used as the basis of this research. This first paper in a series examines experimental data associated with the structure elucidation of a newly separated alkaloid lamellarin g.
A maximum of four structures are shown for information purposes
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Abstract
Thumbnails
Structures
Full Text
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Solvent effect on the spectral properties of Neutral Red
Muhammad A Rauf, Ahmed A Soliman and Muhammad Khattab
Published:13/03/2009 23:26:04
The study was aimed at investigating the effect of various solvents on the absorption spectra of Neutral Red, a dye belonging to the quinone-imine class of dyes. The solvents chosen for the study were water, ethanol, acetonitrile, acetone, propan-1-ol, chloroform, nitrobenzene, ethylene glycol, acetic acid, DMSO and DMF. The results have shown that the absorption maxima of dyes are dependent on solvent polarity. In non-hydrogen-bond donating solvents, solvation of dye molecules probably occurs via dipole-dipole interactions, whereas in hydrogen-bond donating solvents the phenomenon is more hydrogen bonding in nature. To estimate the contribution of the different variables on the wave number of the Neutral Red dye, regression analyses using the ECW model were compared with the π* scale model. This showed that the unified scale for estimating the solvent effect on the absorption of the Neutral Red dye is more adopted and more applicable than the π* scale model.
A maximum of four structures are shown for information purposes
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Abstract
Thumbnails
Structures
Full Text
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Computer-assisted methods for molecular structure elucidation: Realizing a spectroscopist’s dream.
Mikhail Elyashberg§, Kirill Blinov§, Sergey Molodtsov, Yegor Smurnyy§, Antony J. Williams†* and Tatiana Churanova§
Published:19/03/2009 15:50:50
This article coincides with the 40 year anniversary of the first published works devoted to the creation of algorithms for computer-aided structure elucidation (CASE). The general principles on which CASE methods are based will be reviewed and the present state of the art in this field will be described using, as an example, the expert system Structure Elucidator. The developers of CASE systems have been forced to overcome many obstacles hindering the development of a software application capable of drastically reducing the time and effort required to determine the structures of newly isolated organic compounds. Large complex molecules of up to 100 or more skeletal atoms with topological peculiarity can be quickly identified using the expert system Structure Elucidator based on spectral data. Logical analysis of 2D NMR data frequently allows for the detection of the presence of COSY and HMBC correlations of “nonstandard” length. Fuzzy structure generation provides a possibility to obtain the correct solution even in those cases when an unknown number of nonstandard correlations of unknown length are present in the spectra. The relative stereochemistry of big rigid molecules containing many stereocenters can be determined using the StrucEluc system and NOESY/ROESY 2D NMR data for this purpose. The StrucEluc system continues to be developed in order to expand the general applicability, provide improved workflows, usability of the system and increased reliability of the results. It is expected that expert systems similar to that described in this paper will receive increasing acceptance in the next decade and will ultimately be integrated directly to analytical instruments for the purpose of organic analysis. Work in this direction is in progress. In spite of the fact that many difficulties have already been overcome to deliver on the spectroscopist’s dream of “fully automated structure elucidation” there is still work to do. Nevertheless, as the efficiency of expert systems is enhanced the solution of increasingly complex structural problems will be achievable.
A maximum of four structures are shown for information purposes
|
Abstract
Thumbnails
Structures
Full Text
|
|
Applications of Computer-Aided Methods of Structure Elucidation to the Revision of Chemical Structures. I. Structure Revision of Lamellarin g.
M. E. Elyashberg+, K. A. Blinov+, S.G. Molodtsov+, T.S. Churanova+, A.J. Williams.
Published:18/03/2009 11:20:33
The structure elucidation of new organic compounds is clearly one of the most common challenges for organic chemistry and the application of spectroscopy. Molecular structures are usually established on the basis of the combined treatment of data obtained from MS, NMR, IR and UV spectra. Among the various spectroscopic methods 2D NMR spectroscopy now plays an outstanding role in the process of structure determination and is a rich source of structural information. This information however is fuzzy by nature and different researchers can interpret the data in different ways. As a result, it is quite common that structures published in the literature by one group of researchers can be revised by another group. It can be expected that the number of incorrectly identified structures may be reduced if Computer Assisted Structure Elucidation systems (CASE) are used for the purpose of structure elucidation. To familiarize the chemistry community with the advantages of the methodology underpinning CASE systems we will present a series of articles in this journal where we shall try to show the readers how the application of an expert system can prevent a scientist from arriving at an incorrect structural solution and can reduce the time and effort necessary to elucidate a new organic compound. Our expert system Structure Elucidator will be used as the basis of this research. This first paper in a series examines experimental data associated with the structure elucidation of a newly separated alkaloid lamellarin g.
A maximum of four structures are shown for information purposes
|
Abstract
Thumbnails
Structures
Full Text
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Isolation, purification, and full NMR assignments of cyclopamine from Veratrum californicum
John E Oatis Jr1, Pam Brunsfeld2, James W Rushing3, Peter D Moeller4, Daniel W Bearden5, Thomas N Gallien6 and George Cooper IV6
Published:13/03/2009 23:29:26
The Hedgehog signaling pathway is essential for embryogenesis and for tissue homeostasis in the adult. However, it may induce malignancies in a number of tissues when constitutively activated, and it may also have a role in other forms of normal and maladaptive growth. Cyclopamine, a naturally occurring steroidal alkaloid, specifically inhibits the Hedgehog pathway by binding directly to Smoothened, an important Hedgehog response element. To use cyclopamine as a tool to explore and/or inhibit the Hedgehog pathway in vivo, a substantial quantity is required, and as a practical matter cyclopamine has been effectively unavailable for usage in animals larger than mice.
A maximum of four structures are shown for information purposes
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Abstract
Thumbnails
Structures
Full Text
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Colour prediction with JSpecView
Robert J. Lancashire and Craig A.D. Walters
Published:10/03/2010 10:58:45
A routine for the prediction of colour from visible spectra was developed for JSpecView. This involved curve fitting standard colour matching functions (CMF) as well as standard illuminant (D65) data so that visible spectral information, recorded between at least 400 and 700 nm, could be viewed and a prediction made of the colour.
A maximum of four structures are shown for information purposes
|
Abstract
Thumbnails
Structures
Full Text
|
|
Solvent effect on the spectral properties of Neutral Red
Muhammad A Rauf, Ahmed A Soliman and Muhammad Khattab
Published:13/03/2009 23:26:04
The study was aimed at investigating the effect of various solvents on the absorption spectra of Neutral Red, a dye belonging to the quinone-imine class of dyes. The solvents chosen for the study were water, ethanol, acetonitrile, acetone, propan-1-ol, chloroform, nitrobenzene, ethylene glycol, acetic acid, DMSO and DMF. The results have shown that the absorption maxima of dyes are dependent on solvent polarity. In non-hydrogen-bond donating solvents, solvation of dye molecules probably occurs via dipole-dipole interactions, whereas in hydrogen-bond donating solvents the phenomenon is more hydrogen bonding in nature. To estimate the contribution of the different variables on the wave number of the Neutral Red dye, regression analyses using the ECW model were compared with the π* scale model. This showed that the unified scale for estimating the solvent effect on the absorption of the Neutral Red dye is more adopted and more applicable than the π* scale model.
A maximum of four structures are shown for information purposes
|
Abstract
Thumbnails
Structures
Full Text
|
|
Computer-assisted methods for molecular structure elucidation: Realizing a spectroscopist’s dream.
Mikhail Elyashberg§, Kirill Blinov§, Sergey Molodtsov, Yegor Smurnyy§, Antony J. Williams†* and Tatiana Churanova§
Published:19/03/2009 15:50:50
This article coincides with the 40 year anniversary of the first published works devoted to the creation of algorithms for computer-aided structure elucidation (CASE). The general principles on which CASE methods are based will be reviewed and the present state of the art in this field will be described using, as an example, the expert system Structure Elucidator. The developers of CASE systems have been forced to overcome many obstacles hindering the development of a software application capable of drastically reducing the time and effort required to determine the structures of newly isolated organic compounds. Large complex molecules of up to 100 or more skeletal atoms with topological peculiarity can be quickly identified using the expert system Structure Elucidator based on spectral data. Logical analysis of 2D NMR data frequently allows for the detection of the presence of COSY and HMBC correlations of “nonstandard” length. Fuzzy structure generation provides a possibility to obtain the correct solution even in those cases when an unknown number of nonstandard correlations of unknown length are present in the spectra. The relative stereochemistry of big rigid molecules containing many stereocenters can be determined using the StrucEluc system and NOESY/ROESY 2D NMR data for this purpose. The StrucEluc system continues to be developed in order to expand the general applicability, provide improved workflows, usability of the system and increased reliability of the results. It is expected that expert systems similar to that described in this paper will receive increasing acceptance in the next decade and will ultimately be integrated directly to analytical instruments for the purpose of organic analysis. Work in this direction is in progress. In spite of the fact that many difficulties have already been overcome to deliver on the spectroscopist’s dream of “fully automated structure elucidation” there is still work to do. Nevertheless, as the efficiency of expert systems is enhanced the solution of increasingly complex structural problems will be achievable.
A maximum of four structures are shown for information purposes
|
Abstract
Thumbnails
Structures
Full Text
|
|
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