Simplified Protocols

We have presented a simple protocol to run MD simulations for systems of interest. There are, however, some tricks to improve the efficiency and accuracy of molecular dynamics simulations. Some of these techniques, which are discussed later in the book, are today considered standard practice. These methods address diverse issues ranging from efficient force field evaluation to simplified solvent representations. 

When analytes lack the selectivity in the new polar organic mode or reversed-phase mode, typical normal phase (hexane with ethanol or isopropanol) can also be tested. Normally, 20 % ethanol will give a reasonable retention time for most analytes on vancomycin and teicoplanin, while 40 % ethanol is more appropriate for ristocetin A CSP. The hexane/alcohol composition is favored on many occasions (preparative scale, for example) and offers better selectivity for some less polar compounds. Those compounds with a carbonyl group in the a or (3 position to the chiral center have an excellent chance to be resolved in this mode. The simplified method development protocols are illustrated in Fig. 2-6. The optimization will be discussed in detail later in this chapter. 

In particular, the availability of such bacterial biocatalysts in the form of recombinant expression systems [136] in combination with simplified purification protocols opened up this methodology for large-scale applications [204]. 

Example 62 If a manufacturing process involves two raw materials, each defined by three sets of specification limits, and four pieces of equipment with one control knob, then a complete validation protocol would ask for (Three settings Lo, Target, Hi) (2 materials 3 specs + 4 machines 1 control) = 3 = 59 000 experiments, even without repetitions. This product would never reach the market if one did not employ experience and scientific rationale to simplify development by testing only the presumed critical issues, say a total of three specification points for 3 = 27 experiments. 

It is concluded that zeoHte beta can be simultaneously detemplated and Fe-exchanged without FeO formation by treating the parent zeoHte with a Fenton reagent. The catalyst shows good performance on N2O decomposition. This one-pot process simplifies its preparation protocol and can be extended to other systems. Indeed, our approach was followed by Liu et al. [170], for preparing Fe-S BA-15 for benzylation of benzene with interesting results. 

The use of fundamental parameters is attractive for various reasons. They impose fewer restrictions on the number of standards required for analysis. This simplifies the standardisation protocol for maintaining a XRF system, and permits greater flexibility in dealing with different types of materials. Inten-sity/concentration algorithms of the fundamental type, i.e. without recourse to the use of standards, have gradually developed [238-240] and are now widely available [241]. Functionality and quality of XRF software have reached a very high level, with a large variety of evaluation procedures and correction models for quantitative analysis, and calculation of fundamental parameter coefficients for effective matrix corrections. Nevertheless, there is still a need for accuracy improvement of fundamental parameters, such as the attenuation functions. 

Note A simplified protocol of DNA extraction from FFPE tissue may be modified by using heat treatment alone without subsequent purification steps as a one-step protocol boiling the FFPE tissue sections in alkalin solution (0.1 M NaOH) for 20min, cooled down for 15min, and 0.2pF of the retrieval solution is aspirated for PCR test and the remaining sample stored at 4°C for further use. 

For certain substrates, Fokin, Van der Eycken, and coworkers subsequently discovered that the azidation and ligation steps can be carried out in a one-pot fashion, thereby simplifying the overall protocol (Scheme 6.222) [397]. This procedure eliminates the need to handle organic azides, as they are generated in situ. Other applications of microwave-assisted copper(I)-catalyzed azide-alkyne ligations ( click chemistry ) have been reported [398],... 

Wu and Sun have presented a versatile procedure for the liquid-phase synthesis of 1,2, ,4-tctrahydro-/i-carbolines [77]. After successful esterification of the MeO-PEG-OH utilized with Fmoc-protected tryptophan, one-pot cyclocondensations with various ketones and aldehydes were performed under microwave irradiation (Scheme 7.68). The desired products were released from the soluble support in good yields and high purity. The interest in this particular scaffold is due to the fact that the l,2,3,4-tetrahydro-/f-carboline pharmacophore is known to be an important structural element in several natural alkaloids, and that the template possesses multiple sites for combinatorial modifications. The microwave-assisted liquid-phase protocol furnished purer products than homogeneous protocols and product isolation/ purification was certainly simplified. 

Discontinuous approaches are used through necessity in radiometric assays (Oldham, 1993) and in liquid- and gas-chromatography-based protocols (Syed, 1993). Many commercially available kits designed to measure a particular enzyme activity combine absorbance and fluorescence platereader-based technologies with assay protocols that could be done continuously. However, since many users of these kits have little experience in enzymology, assay instructions usually outline a simplified procedure whereby a... 

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