Absorbing potentials, molecular resonances

This work is intended as an introduction to these topics and a tutorial guide to performing quantum chemistry calculations intended to model these types of molecular systems and phenomena. The focus here is on methods that are readily available in standard quantum chemistry software packages and thus, for example, we will discuss the calculation of resonance states using modifications of bound-state methodology, since bound states are what one computes in traditional quantum chemistry. Alternative formalisms such as scattering theory or the explicit treatment of the interaction of a discrete state with a continuum state will not be discussed here. The use of complex absorbing potentials- is discussed only briefly. 

Use of an integrated system incorporating CCC separation, PDA detector, and LC-MS proved to be a valuable tool in the rapid identification of known compounds from microbial extracts.6 This collection of analytical data has enabled us to make exploratory use of advanced data analysis methods to enhance the identification process. For example, from the UV absorbance maxima and molecular weight for the active compound(s) present in a fraction, a list of potential structural matches from a natural products database (e.g., Berdy Bioactive Natural Products Database, Dictionary of Natural Products by Chapman and Hall, etc.) can be generated. Subsequently, the identity of metabolite(s) was ascertained by acquiring a proton nuclear magnetic resonance ( H-NMR) spectrum. 

Infrared spectroscopy exploits the fact that molecules absorb specific frequencies that are characteristic of their structure. These absorptions are resonant frequencies, that is the frequency of the absorbed radiation matches the transition energy of the bond or group that vibrate. The energies are determined by the shape of the molecular potential energy surfaces, the masses of the atoms and the associated vibronic coupling. 

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