Chemical structure JCAMP

The format is general enough that it can be exploited for similar purposes. Thus, a convention exists for describing chemical structures (JCAMP/CS format where CS stands for chemical structure). 

In the case where MS analytical data has been contributed in the other formats, it is prepared into a NIST MS Database, using the NIST MS Search program. This program is used to create MS spectral files from the following electronic formats JCAMP, NIST ASCH, AMDIS, and NIST MS Database. If the analytical data contains no chemical structure, the structure is created in ISIS Draw and then imported into the database as an MOL file. The information associated with the MS analytical data is handled by the NIST program. 

Gasteiger, J. Hendriks, B.M.P. Hoever, P. Jochum, C. Somberg, H. JCAMP-CS. A Standard Exchange Format for Chemical Structure Information in Computer-Readable Form . Submitted for pubhcation in Appl. Spectrosc. 

The formatting of a database involves the creation of several types of files that are manipulated with specialized software. A source file containing raw analytical data is converted to a library file by reducing noise, eliminating unimportant data and compression. Associated exchange files enable data to be transferred in a standard format such as JCAMP/DX for spectrometric data and JCAMP/CS for chemical structures. 

Chemical structure description has been done by following the JCAMP rules too. Today the MDL Information Systems, Inc. software, distributed worldwide, has defined a standard of its own. The Molfile and SDfile or RDfile formats serve as standards for structure exchange and are a more common alternative to the JCAMP format. 

AIA = Analytical Instruments Association AFFN = ASCII free format numeric API = application programming interface ASDF = ASCII squeezed difference form ASMS = American Society of Mass Spectrometry ASTM = American Society for Testing and Materials CCDB = Committee on Chemical Databases CDF = common data form CPEP = Committee on Printed and Electronic Publications CS = chemical structure EPA = United States Environmental Protection Agency lUPAC = International Union of Pure and Applied Chemistry JCAMP-DX = Joint Committee on Atomic and Molecular Physical Data - Data Exchange LDR = labeled data record netCDF = network common data form SMD = standardized molecular data UCAR = University Corporation for Atmospheric Research XDR = external data representation. 

The basic structure of a JCAMP-DX file has developed from the original version 4.24 through the minor variations incorporated in the chemical structure protocol to the radically different structures based on JCAMP-DX version 5.0 as used later for the MS and NMR protocols (Figure 2). 

A major advance Introduced in the JCAMP-CS protocol was interblock linking. Although the compound data file format had been described in JCAMP-DX version 4.24 there was no mechanism provided to cross-reference between blocks. This problem was solved by the introduction of the LDR BLOCKJD=, which could be used to link a spectrum or peak table block to the chemical structure block for instance. 

Some standard ways of storing and transferring chemical structures are proprietary (e.g., MDL s Molfile) others such as the JCAMP-CS format, published by the Joint Committee on Atomic and Molecular Physics, are in the public domain. Barnard (36) refers to some of them in a paper that deals with recent developments in improving the Standard Molecular Data (SMD) file format and work towards establishing it as the one standard for transfer of chemical structure information between systems. In Chapter 11 of this book, Donner et al. describe the SMD format in more detail. Garavelli, in Chapter 12, also discusses SMD, but concentrates on existing standards for molecular modeling systems. 

Recently some other research institutions in the field of computer chemistry exhibited distinct interest in the SMD format (e.g., Fraser Williams, ORAC Ltd, FIZ Chemie Berlin, Sadtler and others) and compatible formats have been designed for special purposes. For example there is the format by the Joint Committee on Atomic and Molecular Physics, JCAMP, for spectroscopic data storage which on one hand has a more limited scope, but on the other hand puts much emphasis on spectroscopically relevant features like stereochemistry. (Gasteiger, J. Hendriks, B.M.P. Hoever, P. Jochum, J. Somberg, H. JCAMP-CS. A Standard Exchange Format for Chemical Structure Information in Computer Readable Form , to be published). 

A new project on electronic publishing, financially supported by the German Ministry of Research, and worked out by Wiley-VCH/Chemical Concepts, uses JCAMP and MDL standards (Figure 1). Spectroscopic data acquired directly from the spectrometer site are converted to the JCAMP format. The software TranSpec allows structure input or import in Molfile format. Quality control modules check the reliability of the information. The files in JCAMP and MDL formats are sent to the data server by email. Special software extracts the data from the email automatically and handles the entry into the database. 

---