Molecular fingerprinting

SALI compares fiivorably with other major surface analytical techniques in terms of sensitivity and spatial resolution. Its major advantj e is the combination of analytical versatility, ease of quantification, and sensitivity. Table 1 compares the analytical characteristics of SALI to four major surfiice spectroscopic techniques.These techniques can also be categorized by the chemical information they provide. Both SALI and SIMS (static mode only) can provide molecular fingerprint information via mass spectra that give mass peaks corresponding to structural units of the molecule, while XPS provides only short-range chemical information. XPS and static SIMS are often used to complement each other since XPS chemical speciation information is semiquantitative however, SALI molecular information can potentially be quantified direedy without correlation with another surface spectroscopic technique. AES and Rutherford Backscattering (RBS) provide primarily elemental information, and therefore yield litde structural informadon. The common detection limit refers to the sensitivity for nearly all elements that these techniques enjoy. 

One of the most common uses of vibrational spectroscopy is as a molecular fingerprinting tool whereby spectral features are assigned to the presence of particular fragments in molecules. These assignments are, however, only... 

Variable numbers of randomly repeated (VNTR) units are one common type of insertion that results in an RFLP. The VNTRs can be inherited, in which case they are useful in estabhshing genetic association with a disease in a family or kindred or they can be unique to an individual and thus serve as a molecular fingerprint of that person. 

Why is a molecular absorption spectrum called a molecular fingerprint ... 

IR spectra are characterized by rather sharp absorption bands and each such band is characteristic of a particular covalent bond in the sample molecule. An example is shown in Figure 8.14. Thus, while IR spectra are molecular fingerprints, as are UV-VIS spectra, they have a greater worth to a qualitative analysis scheme due to the specificity of the absorption bands. 

The primary use of NMR is in the determination of the structure of unknown organic compounds. It is often used in conjunction with other spectrometric techniques (FTIR and mass spectrometry, for example) in this determination. NMR spectra are molecular fingerprints, however, and by comparison with data files of known spectra, the structure of an unknown can be determined independent of other data. 

Because the fragmentation pattern produced by a mass spectrometer can be used as a fingerprint of molecule, the mass spectrum reveals, for example, whether the correct compound has been synthesized and whether contaminants are present. One can see that it is a molecular fingerprint, just as absorption spectra are molecular fingerprints, and that it is a powerful tool for identification purposes. 

Similar Both are molecular fingerprints and therefore useful for qualitative analysis, and both display absorption behavior over a wavelength range. 

Viswanadhan, V. N., Ghose, A. K., Singh, U. C., and Wendoloski, J. J. (1999) Prediction of solvation free energies of small organic moleucles additive-constitutive models based on molecular fingerprints and atomic constants.. /. Chem. Inf. Comput. Sci. 39, 405-412. 

Studies by Teplyakov et al. provided the experimental evidence for the formation of the Diels-Alder reaction product at the Si(100)-2 x 1 surface [239,240]. A combination of surface-sensitive techniques was applied to make the assignment, including surface infrared (vibrational) spectroscopy, thermal desorption studies, and synchrotron-based X-ray absorption spectroscopy. Vibrational spectroscopy in particular provides a molecular fingerprint and is useful in identifying bonding and structure in the adsorbed molecules. An analysis of the vibrational spectra of adsorbed butadiene on Si(100)-2 x 1 in which several isotopic forms of butadiene (i.e., some of the H atoms were substituted with D atoms) were compared showed that the majority of butadiene molecules formed the Diels-Alder reaction product at the surface. Very good agreement was also found between the experimental vibrational spectra obtained by Teplyakov et al. [239,240] and frequencies calculated for the Diels-Alder surface adduct by Konecny and Doren [237,238]. 

Because of the numerous choices for molecular descriptors, weighting factors, and similarity coefficients, there are many ways in which the similarities between pairs of molecules can be calculated. The most used molecular descriptors for defining similarity are probably the 2D fingerprints (22). The bit strings of the molecular fingerprints are used to calculate similarity coefficients. Table 2.3 lists several selected similarity coefficients that can be used with various 2D fingerprints (23). The Tanimoto coefficient is the most popular one (22). 

Since LEAP1 was built based on Pipeline Pilot technology, multiple molecular fingerprints and similarity methods can be applied at disposal, which currently include MDL Public Keys and different levels of FCFPs and ECFPs (18). 

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