Molecular data

Description by rotational lists was introduced by Cook and Rohde [110] in the specification of the Standard Molecular Data (SMD) format [111]. In this stereochemical approach, the basic geometrical arrangements around a stcrcoccntcr arc defined in a list (c.g., square, tetrahedron, etc.). The atoms in those stcrcoclcmcnts are also labeled with numbers in a pre-defined way (Figure 2-72),... 

Any one of these additivity schemes can be used for the estimation of a variety of thermochemical molecular data, most prominently for heats of formation, with high accuracy [13]. A variety of compilations of thermochemical data are available [14-16]. A computer program based on Allen s scheme has been developed [17, 18] and is included in the PETRA package of programs [19]. 

A most important task in the handling of molecular data is the evaluation of "hidden information in large chemical data sets. One of the differences between data mining techniques and conventional database queries is the generation of new data that are used subsequently to characterize molecular features in a more general way. Generally, it is not possible to hold all the potentially important information in a data set of chemical structures. Thus, the extraction of relevant information and the production of reliable secondary information are important topics. 

Moli cii lar dynamics is csscn Lially a sLiidy of ih c evniiitioii in tim c of energetic and siniclnral molecular data. The data is often best represented as a graph of a molecular quantity as a function of iime. The values to be plotted can be any qnantity x that is being averaged over the trajectory, or the standard deviation. Dx. You can create as many as four simultaneous graphs at once. 

With all this in mind, the molecular data in column 3 of Table 18.9 has been corrected to 298 K and 1 atm pressure. Like is compared to like in Table 18.10. 

The group centred around M. J. S. Dewar has used a combination of (2) and (3) for assigning parameter values, resulting in a class of commonly used methods. The molecular data used for parameterization are geometries, heats of formation, dipole moments and ionization potentials. These methods are denoted modified as their parameters have been obtained by fitting. 

MNDO has been parameterized for the elements H, B, C, N, O, F, Al, Si, P, S, Cl, Zn, Ge, Br, Sn, I, Hg and Pb. The G s, Gsp, Gpp, Gp2, H p parameters are taken from atomic spectra, while the others are fitted to molecular data. Although MNDO has been succeeded by the AMI and PM3 methods, it is still used for some types of calculation where MNDO is known to give better results. 

Considering that the parameters for the MNDO/d method for all first row elements (which are present in most of the training set of compounds) are identical to MNDO, the improvement by addition of d-functions is quite impressive. It should also be noted that MNDO/d only contains 15 parameters, compared to 18 for PM3, and that some of the 15 parameters are taken from atomic data (analogously to the MNDO/AMl parameterization), and not used in the molecular data fitting as in PM3. 

In the biosciences, a database is a curated repository of raw data containing annotations, further analysis, and links to other databases. Examples of databases are the SWISSPROT database for annotated protein sequences or the FlyBase database of genetic and molecular data for Drosophila melanogaster. 

R. H. Sherman and W. F. Giauque, "Arsine. Vapor Pressure, Heat Capacity, Heats of Transition, Fusion, and Vaporization. The Entropy from Calorimetric and from Molecular Data", J. Am. Chem. Soc., 77, 2154-2160 (1955). 

P10.2 Given the following molecular data for perchloryl fluoride. (Perchloryl fluoride (CIO3F) is tetrahedral with three oxygens and a fluorine bonded to a central chlorine. ... 

Table A4.1 Thermodynamic functions of an ideal gas. (Use R = 8.314510 J-K l mol 1 and SI units for pressure, temperature, and all molecular data.)...

The crystal structures of the mesogenic compounds CBn were reported by different authors [45-51]. Selected crystallographic and molecular data of the investigated compounds CBn are summarised in Table 1. Only the crystal structures of some compounds will be discussed here. 

Table 1. Crystal and molecular data of mesogenic 4 -n-alkyl-4-cyanobiplienyls (CBn)... 

In this section, we will describe the crystal structures of the mesogenic A -n-alkoxy-4-cyano-biphenyls (Fig. 1) [53-57]. The compounds have the phase sequences crystal-nematic-isotropic for CB05—CB07 and monotropic nematic for CB01-CB04 crystal-smectic A-nematic-isotropic for CB08. The crystal and molecular data of the investigated compounds CBOn are summarised in Table 2. 

Zugenmaier and Heiske [60] presented the crystal and molecular structures of the homologous series of 4 -(hydroxy-l-n-alkoxy)-4-cyanobi-phenyls (CBO(CH2)nOH) n = 4, 5, 7-11). The chemical structure of the compounds is shown in Fig. 1. All compounds of the series exhibit a nematic phase. The crystal and molecular data of the investigated compounds CBO(CH2)nOH and some derivatives are presented in Table 3. 

The synthesis of the mesogenic trans-4-n-alkyl-(4 -cyanophenyl)-cyclohexanes (PCHn) was described by Eidenschink et al. [65] in 1977. Most of the compounds exhibit a nematic phase close to room temperature. The chemical structure of the mesogenic PCHn is shown in Fig. 6. During the past few years, the crystal structures of some mesogenic phenylcyclohexanes were published [66-70]. Selected crystallographic and molecular data of the investigated compounds PCHn are presented in Table 4. 

The crystal and molecular data of the investigated 2,5-diphenyl pyrimidines are presented in Table 7. The molecules of both compounds adopt a stretched form. In the case of compound 2-PPePP, the pyrimidine ring is approximately coplanar with the phenyl rings attached to it in the 2- and 5-positions. By contrast, the phenyl rings are twisted with respect to the central pyrimidine ring in 5-PBuPP. 

Table 10. Crystal and molecular data of the mesogenic 4 -cyanophenyl-4-n-alkylbenzoates (CPnB), 4 -cyanophenyl-4-n-alkoxybenzoates (CPnOB), and 4 -n-alkoxyphenyl-4-cyanobenzoates (nOPCB)...

Kelly, S., Foley, B., Dunford, L., Coughlan, S., Tuite, G., Duffy, M., Mitchell, S., Smyth, B., O Neill, H., McKeown, P., Hall, W., and Lynch, M. (2008). Establishment of a national database to link epidemiological and molecular data from norovirus outbreaks in Ireland. Epidemiol. Infect. 136, 1472-1479. 

S. Matt, T. Fiegele, G. Hanel, D. Muigg, G. Denifl, K. Becker, H. Deutsch, O. Echt, N. Mason, A. Stamatovic, P. Scheier, and T. D. Mark, AlP Conference Proceedings 2000, 543 (Atomic and Molecular Data and Their Applications), 191. 

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