Standard molecular data structure

The attention of software developers and users is drawn to current problems in redirecting all data input to be read from files and in allowing alternative entry points which avoid repeated initialisation. They are urged to make more use of the Standard Molecular Data (SMD) format for transfer of structure data. 

During the past few years interest has grown in the development of standard formats for the machine-readable presentation of chemical structures, and a few proposals have been published. One of these is the Standard Molecular Data (SMD) format, developed by a group of European chemical companies. Under the auspices of the Chemical Structure Association, a series of technical working groups have examined the original version of SMD format and proposed a number of revisions and extensions. This poster paper describes the revised version of the format using annotated examples, and discusses the areas where further extension is required. 

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. 

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. 

Molecular dynamics is essentially a study of the evolution in time of energetic and structural molecular data. The data is often best represented as a graph of a molecular quantity as a function of time. The values to be plotted can be any quantity x that is being averaged over the trajectory, or the standard deviation, Dx. You can create as many as four simultaneous graphs at once. 

An important characteristic of ab initio computational methodology is the ability to approach the exact description - that is, the focal point [11] - of the molecular electronic structure in a systematic manner. In the standard approach, approximate wavefunctions are constructed as linear combinations of antisymmetrized products (determinants) of one-electron functions, the molecular orbitals (MOs). The quality of the description then depends on the basis of atomic orbitals (AOs) in terms of which the MOs are expanded (the one-electron space), and on how linear combinations of determinants of these MOs are formed (the n-electron space). Within the one- and n-electron spaces, hierarchies exist of increasing flexibility and accuracy. To understand the requirements for accurate calculations of thermochemical data, we shall in this section consider the one- and n-electron hierarchies in some detail [12]. 

In general, standard methods applicable to a vast majority of compounds of interest to ensure throughput capabilities are critical for LC/MS screens. Although not optimized for specificity, standard conditions provide a systemic measure of control. This control results in data that has high quality, reliability, and comparability. With a strategic selection of compounds that have similar molecular weights, structural features, and chromatographic properties, the detection selectivity and precision are satisfactory for this particular type of analysis. 

Standard molecular mechanics (MM) force fields have been developed that provide a good description of protein structure and dynamics,21 but they cannot be used to model chemical reactions. Molecular dynamics simulations are very important in simulations of protein folding and unfolding,22 an area in which they complement experiments and aid in interpretation of experimental data.23 Molecular dynamics simulations are also important in drug design applications,24 and particularly in studies of protein conformational changes,25,26 simulations of the structure and function of ion channels and other membrane proteins,27-29 and in studies of biological macromolecular assemblies such as F-l-ATPase.30... 

The physical and chemical properties of the drug substance must be described in detail, including appearance, physical form, solubility, melting and/or boiling points, molecular weight, structural and molecular formulas, and Wisswesser line notation (WLN). Where applicable, provide information on isomers, polymorphs, pKa values, and pH. Include, in brief, the data obtained and reference standard(s) used to elucidate the structure of the drug substance. 

NIST Resources. The National Institute of Standards and Technology has a Standard Reference Data Program that maintains electronic databases on Analytical chemistry, Atomic and molecular physics, Biotechnology, Chemical and crystal structure. Fluids, Materials properties. Surface data, and Thermochemical data. Some of these databases are available at moderate cost as PC products (diskettes, CD-ROMs, or Internet downloads) and some are free online systems. Further information is available on the website www. nist.gOv/srd/ begin.htm. 

Only a few X-ray diffraction and XAFS studies at high temperatures can be found in the literature mainly due to technical difficulties in experimental work. E.g. Okamoto et al. (1998, 1999) measured the X-ray diffraction of some molten rare earth and uranium trihalides. The obtained X-ray diffraction data were analyzed using molecular dynamics technique. This procedure is almost standard in the structural analysis of molten salt systems. 

The MST/EPA/NIH Mass Spectral Library 1998 database ( www.nist.gov/ srd/analv.htm) is the product of a muftiyear, comprehensive evaluation and expansion of the world s most widely used mass spectral reference library, and is sold in ASCII or Windows versions. It contains 108,000 compounds with electron ionization spectra, chemical structures, and molecular weights. It is available with the NIST MS Search Program for GC/MS deconvolution, MS interpretation, and chemical substructure analysis. The NIST chemistry WebBopk ( http //webbook.nist.gov) is a. free online system that contains the mass spectra of over 12,000 compounds (this Standard Reference Data Program also has IR and UV-Vis spectra). 

In most papers referenced above, the standard molecular formulation of the B3LYP functional has been employed, and its results graded against a set of other Hamiltonians available in CRYSTAL. These usually include at least HP, LDA and one GGA functional (PW or PBE), and thus enable a critical appraisal of the B3LYP performance compared to other well established Hamiltonians in solid-state chemistry. Several observables have been examined, such as the equilibrium structure, elastic constants and bulk moduli, thermochemical data, electric field gradients, phonon spectra and vibrational frequencies, polarisation of the ferroelectric phases, magnetic coupling in open-shell transition metal oxides. We shall comment on each observable separately. 

Since it is a non-quantum mechanical method, molecular mechanics is not intrinsically well suited to treating reaction mechanisms other than "reactions" that are simply conformational changes. That is, it would be completely unreasonable to study a bond-breaking process using a standard molecular mechanics package, because the method was not at all parameterized to treat bond-broken structures. Similarly, we might expect that an insufficient data base would exist to allow the development of reliable molecular mechanics parameters for reactive intermediates. Nevertheless, in some specific cases the method has been applied successfully to the evaluation of reaction mechanisms. 

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