Dialog integration

Chem comes with default parameter sets, Amber2 and Amber3 in the case of the AMBER method. It is possible, however, to define an arbitrary number of additional parameter sets for the AMBER method (or for any of the other three force field methods). These user-defined parameter sets can be specified in the Parameters dialog box and integrated into HyperChem, in the same way as the default sets. 

The developers of ZINDO found that the parameters required to reproduce orbital energy orderings and UV spectra are different from those required to reproduce accurate structures by geometry optimization. They introduced anew pair of parameters, called the overlap weighting factors, to account for this. These parameters are provided in HyperChem in the Semi-empirical Options dialog box. Their effect is to modify the resonance integrals for the off-diagonal elements of the Fock matrix. 

HyperChem includes a number of time periods associated with a trajectory. These include the basic time step in the integration of Newton s equations plus various multiples of this associated with collecting data, the forming of statistical averages, etc. The fundamental time period is Atj s At, the integration time step stt in the Molecular Dynamics dialog box. 

Automatic Calls a dialog box to control the automatic integration, which can be carried out for either the whole spectrum or for automatically fixed regions. Automatic detection of integration regions is controlled by four parameters. Use the Help option for details. 

Regions Opens the Integral Regions dialog box with a list of all of the defined... 

Report This button opens the Report Integrals dialog box where the numerical... 

Use first the left mouse button to click the Integration button in the button panel and perform a quick automatic integration. Click then the Integration button with the right mouse button to try the option for rapid parameter adjustments and start the integration with the Execute button in the corresponding dialog box. 

In the Analysis pull-down menu choose the Integration option. Clicking on the Automatic button in the corresponding button panel opens a dialog box. Select the Detect Area mode and click on the Execute button to perform an automatic integration. 

Note Equal slopes of the integral baseline may by corrected with the Bias option. It is recommended to apply a spectrum baseline correction (see chapter 5) or to simply activate the Basline Correction option in the integral Options dialog box prior to integration. 

Repeat the integration but activate the Baseline Correction mode in the Options... dialog box, and compare the two results. 

To calibrate this single integral choose the Options... dialog box and set the All Integrals parameter to the value 22, the total number of protons for peracetylated glucose. 

Activate the Options... button again and set the Common Offset to 10%. Try out the other Display and Miscellaneous options in the dialog box. Select various integrals and try out the Scaling button. Adjust the integrals to suit your requirements. 

This button opens a dialog box in which you may select the font to be used in plotter or preview output for the spectrum window (scale, peak picking, integral). It does not affect the fonts for the parameter and the title window. 

A full report of the defined integrals can be listed in a report dialog box, including the size or width of the integral region (in data points), the start and end rows and columns (number and ppm), the integral value (absolute, normalised) and the calculation mode used. 

The setup of experiment parameters can be separated in different categories. The entry of experiment parameters is not just restricted to the dialog box of the Go I Check Experiment Parameters pull-down menu command. The rf channel option bar is an integral part of the NMR-SIM main window whilst the Parameters I... pull-down menu command opens several different dialog boxes. The various different categories of experiment parameters are listed in Table 4.4. 

DBMS Design, Selection, and Systems Integration 116 4. DIALOG GENERATION AND MANAGEMENT SYSTEMS 131... 

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