Known molecules

Another technique employs a database search. The calculation starts with a molecular structure and searches a database of known spectra to find those with the most similar molecular structure. The known spectra are then used to derive parameters for inclusion in a group additivity calculation. This can be a fairly sophisticated technique incorporating weight factors to account for how closely the known molecule conforms to typical values for the component functional groups. The use of a large database of compounds can make this a very accurate technique. It also ensures that liquid, rather than gas-phase, spectra are being predicted. 

Determination of surface functional groups, e.g., —OH, —C - C—, and >C = O, and identificadon of adsorbed molecules comes principally from comparison with vibrational spectra (infixed and Raman) of known molecules and compounds. Quick qualitative analysis is possible, e.g., stretching modes involving H appear for v(C—H) at 3000 cm and for v(0—H) at 3400 cm L In addition, the vibrational energy indicates the chemical state of the atoms involved, e.g., v(C=C) " 1500 cmT and v(C=0) " 1800 cm"L Further details concerning the structure of adsorbates... 

The vast majority of known molecules are organic, totally lacking in symmetry and having singlet electronic ground states which can be written in the language of elementary descriptive chemistry as configurations Am-... 

Known molecules queried with n biotransformation rules to annotate observed metabolites as a binary bit string... 

C09-0133. Among the halogens, only one known molecule has the formula X 7. It has pentagonal bipyramidal geometry, with five Y atoms in a pentagon around the central atom X. The other two Y atoms are in axial positions. Draw a ball-and-stick model of this compound. Based on electron-electron repulsion and atomic size, determine the identities of atoms X and Y. Explain your reasoning. (Astatine is not involved. This element is radioactive and highly unstable.)... 

Verification, determination and quantification of known molecules Stmcture confirmation... 

Molecules that are structurally similar (e.g., enantiomers) to previously known molecules (e.g., racemates) may, in a fact-dependent fashion, be patentable. Work with your patent professional early in the process to determine if such molecules are worth pursuing as program targets. 

The electronic structure and physical properties of any molecule can in principle be determined by quantum-mechanical calculations. However, only in the last 20 years, with the availability and aid of computers, has it become possible to solve the necessary equations without recourse to rough approximations and dubious simplifications2. Computational chemistry is now an established part of the chemist s armoury. It can be used as an analytical tool in the same sense that an NMR spectrometer or X-ray diffractometer can be used to rationalize the structure of a known molecule. Its true place, however, is a predictive one. Therefore, it is of special interest to predict molecular structures and physical properties and compare these values with experimentally obtained data. Moreover, quantum-mechanical computations are a very powerful tool in order to elucidate and understand intrinsic bond properties of individual species. 

In this case study, we will start with a known molecule (for example, Corticosterone), use the property estimation features in ProPred [Marerro (2002)] to create free attachments in the molecule (that is, create a backbone). The Backbone is then transferred to ProCamd, where terminated structures will be generated. In this way structures of synthetic candidates of a lead biologically active compound may be identified through molecular design. 

This system exhibits a local minimum with attachment of the SiH moiety to the C5H5 ring however, the global minimum corresponds to the known molecule silabenzene (36) ... 

C5H5P, namely an n local minimum but with the known molecule. 

Electronic databases of the mass spectral fragmentation patterns of known molecules can be rapidly searched by computer. The pattern and intensity of fragments in the mass spectrum is characteristic of an individual compound so comparison of the experimental mass spectrum of a compound with those in a library can be used to positively identify it, if its spectrum has been recorded previously. 

Because of the current availability of such programs, we thought it would be useful to provide the organic chemist with examples of how the method might be used, as well as to describe, in hopefully understandable terms, the model in which the calculation of IR spectra is based. In Section 2 the model is introduced and its reliability is demonstrated by comparison of the computed spectra with those observed for several well-known molecules. In Section 3 examples of the use of computed IR spectra in the identification of reactive molecules are presented, and in Section 4 those of reactive intermediates. 

Crowther, R. A. and Blow, D. M. (1967) A method of positioning a known molecule in an unknown crystal structure. Acta Crystallogr. 23, 544-548. 

The CIP system evolved in four steps by a combination of logical reasoning and a pragmatic trial and error approach. The evolution was driven by the practical necessity to describe the vast number of known molecules and an impressive array of brain-teasers proposed by clever chemists. 

The molar absorptivity (e) of a known molecule is constant under identical conditions of solvent, concentration and path length, and can be used to quantify the amount of a particular pharmaceutical in a tablet. Such assays form the basis of many quality assurance procedures in the pharmaceutical industry, and have been extensively used by the British Pharmacopoeia (B.P.). More recently, however, high-performance liquid chromatography (HPLC) has replaced UV analysis in many B.P. assays, as most industrial analyses routinely use HPLC. 

With experience one comes to recognize the point group to which a molecule belongs simply by analogy with some other known molecule. However, until one builds up a memory file of the point groups of representative molecules, it is best to use some systematic method. A scheme which will enable the reader to do this is shown in Table 3-7.1 and to illustrate how it works, we will consider three typical cases. 

Well-known molecules with an alkane or alkanon group are the saccharides, with the even better known examples glucose and fructose. A saccharide contains 5 or 6 C atoms, an alkane or alkanon group and an OH group at the remaining C atoms (Fig. 3.19). 

Molecules and polyatomic ions in which the octet is exceeded -sometimes called hypervalent species - present problems. Many well-known molecules such as PF5, SF6 and C1F3 cannot be represented by Lewis structures which obey the octet rule. VB descriptions of hypervalent species can be devised by postulating hybridisation schemes... 

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