Print spectra

The Print pull-down menu (Fig. 13.1) contains the functions for printing spectra and reports. However, before you can start to print spectra you first have to define a printer. We assume that a printer is already installed on your computer. 

Use the Print Setup command from the Print menu to define the printer and the print parameters like paper size and print quality (see Fig. 6.7). Clicking on the Properties button opens another dialog box. The settings shown will depend on the model of your printer. 

The command Print Spectra uses a template to create a plot of spectra and all associated parameters. After loading as usual the relevant spectrum into the window of the Select Files page of the Plot Spectra dialog box (Fig. 13.2), it is necessary to choose a page layout. Hence, use the Change Layout button to select a template from the folder OPUSDEMO Scripts (see Fig. 13.3). To inspect the final layout prior to plotting, click on the Preview button to open another window that shows an exact copy of the subsequent plot. An example of such a print preview is displayed in Fig. 13.4. 

IR and Raman Spectroscopy Fundamental Processing. Siegfried Wartewig Copyright 2003 WILEY-VCH Verlag GmbH Co. KGaA, Weinheim ISBN 3-527-30245-X 

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Different capillary columns are available for organic acid separation and analysis. In our laboratory, the gas chromatography column in all GC-MS applications is crosslinked 5% phenyl (poly)methyl silicone, 25 m internal diameter 0.20 mm stationary phase film thickness 0.33 pm (Agilent HP-5, DB-5, or equivalent). Several instrument configurations are commercially available, which allow for positive identification of compounds by their mass spectra obtained in the electron impact ionization mode. A commercially available bench-top GC-MS system with autosampler (Agilent 6890/5973, or equivalent) is suitable. Software for data analysis is available and recommended. The use of a computer library of mass spectra for comparison and visualization of the printed spectra is required for definitive identification and interpretation of each patient specimen. 

Many digital spectral libraries have been transformed from printed spectra collections. Well known printed collections are the Aldrich spectra collection [1], the Sadder spectra collection [2-4], the Schrader-Meyer Adas of IR and Raman spectra [5], the Hummel collection of IR spectra of polymers [6], the Merck IR Adas [7] and the Buback collection of NIR spectra [8]. IR spectra have the largest share of digital optical spectra, followed at a clear distance by Raman spectra. Larger collections of UV/VIS spectra have not been estabhshed due to their missing fingerprint capability and to the strong sensitivity of the UV/VIS spectra to solvent interactions. A variety of dedicated spectra collections have been created in industrial laboratories without access to the public. 

Finally, Chapter 13 outlines how to print spectra and reports. 

When UV spectra are used for qualitative identification of a compound, the identification is carried out by comparing the unknown compound s absorption spectrum with the spectra of known compounds. Compilations of UV absorption spectra in electronic formats can be found from commercial sources such as the Informatics Division, Bio-Rad Laboratories (www.bio-rad.com), or the American Petroleum Institute (API) indices. Computer searching and pattern matching are the ways spectra are compared and unknowns identified in modern laboratories. Some academic libraries still maintain the printed spectra collections, which must be searched manually. 

The Beer-Lambert rules derived above (equation 7.3) apply equally to absorption of infrared radiation by molecules. Moreover, infrared absorption spectra possess an advantage over the more common ultraviolet absorption in the greater number of bands present. It is often possible to select an absorption band for each component of a mixture such that little or no interference occurs between them. For these reasons, infrared spectroscopy is often used quantitatively in the analytical laboratory to determine drug concentrations in solution. A calibration curve for the assay may be obtained (and Beer s law confirmed) by converting the printed spectrum... 

Compare the spectrum with a vahdated finger print spectrum or with results predicted based on the primary sequence. 

The absorption spectra were obtained with either a Hewlett-Packard 84S0A or 8451A diode array qiectrophotometer and plotted as a wavelength versus transmittance from 220 nm to 340 nm. Sample sdutions were prepared by dissolving an appropriate amount of chemical into die proper solvent. In die printed spectrum, the solvent solutions are represented by a solid line for die O.2NH2SO4 solu-... 

Alternative procedure Mathcad. Follow the procedure above except that where QMOBAS is indicated, use Mathcad instead. Enter the Huckel molecular orbital matrix, modified by subtracting xl, with some letter name. For example, call the modified matrix A. Type the command eigenvals(A) = with the name of the modified HMO matrix in parentheses. Mathcad prints the eigenvalues. The command eigenvecs(A) yields the eigenvectors, which are useful in ordering the energy spectrum. 

The essential features of an NMR spectrometer shown m Figure 13 5 are not hard to understand They consist of a magnet to align the nuclear spins a radiofrequency (rf) transmitter as a source of energy to excite a nucleus from its lowest energy state to the next higher one a receiver to detect the absorption of rf radiation and a recorder to print out the spectrum... 

In a process similar to that described in the previous item, the stored data can be used to identify not just a series of compounds but specific ones. For example, any compound containing a chlorine atom is obvious from its mass spectrum, since natural chlorine occurs as two isotopes, Cl and Cl, in a ratio of. 3 1. Thus its mass spectrum will have two molecular ions separated by two mass units (35 -i- 2 = 37) in an abundance ratio of 3 1. It becomes a trivial exercise for the computer to print out only those scans in which two ions are found separated by two mass units in the abundance ratio of 3 1 (Figure 36.10). This selection of only certain ion masses is called selected ion recording (SIR) or, sometimes, selected ion monitoring (SIM, an unfortunate... 

Once the peaks have been collected and stored, the computer can be asked to work on the data to produce a mass spectrum and print it out, or it can be asked to carry out other operations such as library searching, producing a mass chromatogram, and making an accurate mass measurement on each peak. Many other examples of the use of computers to process mass data are presented in other chapters of this book. 

A data system stores the mass spectrum until required, when it can be printed at leisure or viewed immediately on the computer screen. 

This problem is known as dead time. To offset this effect, an algorithm is used to adjust the actual number of events into a true number of events. Since the numbers of ions represent ion abundances, the correction adjusts only abundances of ions before a mass spectrum is printed. 

Once the mass spectral information has been acquired, various software programs can be employed to print out a complete or partial spectrum, a raw or normalized spectrum, a total ion current (TIC) chromatogram, a mass chromatogram, accurate mass data, and metastable or MS/MS spectra. 

A valuable source of up-to-date reviews of many aspects of MSE is a series of books. Annual Reviews of Materials Science, published for the last 30 years. There has been one extensive series of high-level multiauthor treatments right across the entire spectrum of MSE, in the form of 25 books collectively entitled Materials Science and Technology A Comprehensive Treatment (1991-2000), masterminded by Peter Haasen, Edward Kramer and myself. There have also been three encyclopedias, the Encyclopedia of Materials Science and Engineering (1986), the Encyclopedia of Advanced Materials (1994) and the Encyclopedia of Materials (2001), which last has appeared in both printed and on-line versions and will receive annual updates. 

The infrared absorption spectrum of a compound may be regarded as a sort of finger-print of that compound see Fig. 19.1. Thus for the identification of... 

Optimum values for the probabilities may not be obtained in the case that experimental llnewidths in the spectrum are very different since only a single linewidth is used for the simulated spectra. The calculated probabilities may be stored in the database and hard copy reports may be printed-... 

Figure 3a shows the spectra of CO adsorbed at room temperature on a typical Cr(II)/Si02 sample. At low equilibrium pressure (bold black curve), the spectrum shows two bands at 2180 and 2191 cm Upon increasing the CO pressure, the 2191 cm component grows up to saturation without frequency change. Conversely, the 2180 cm component evolves into an intense band at 2184 cm and a shoulder at 2179 cm The bands at 2191, 2184, and 2179 cm which are the only present at room temperature for pressures lower than 40 Torr, are commonly termed the room temperature triplet and are considered the finger print of the Cr(ll)/Si02 system (grey curve in Fig. 3). A new weak band at around 2100 cm appears at room temperature only at higher CO pressure. As this peak gains intensity at lower temperature, it will be discussed later. The relative intensity of the three components change as a function of the OH content (i.e., with the activation temperature and/or the activation time) [17].

Figures 2 through 9 are design charts for ultraviolet stabilized polycarbonate under blast load. Charts are provided for pane thicknesses of 1/4, 3/8, 1/2, and 1 inch for pane areas up to 25 ft at pane aspect ratios (pane length to width ratios) of 1.00, 1.50, 2.00 and 4.00. The charts relate the peak experienced blast overpressure capacity, B, for convenient pane dimensions across the spectrum of encountered blast durations. Depending on the orientation of the window to the charge, the blast overpressure may either be incident or reflected. The pane dimensions (measured across the span from the gasket centerline) peak blast capacity at 1000 msec, B, static frame design pressure, r, and the required bite are printed to the right...

Figure 10.3. Mass array, (a) Primer binding (b) primer extension enzyme, ddATP and dCTP/ dGTP/dTTP addition (c) primer terminates (d) primer extension products ready for MALDI-MS (e) MS spectrum of primer extension products. Each addition of a nucleotide to the primer extension product increases the mass by 289 to 329 Da, depending on the nucleotide added. The mass difference is easily resolved by MALDI-TOF, which has the ability to detect differences as small as 3 Da. Printed by kind permission of Sequenom. (See color insert.)...

Another benefit of the fluorinated layer is its excellent adhesion properties. Printing (including water-based inks) and labels will normally adhere tenanciously to a fluorinated layer. In some cases it is even possible to fluorinate printed containers without discoloration ofthe printing. In these cases the printing will be far more insoluble to a large spectrum of solvents and will then only be removed with difficulty. 

One of the important functions of the infrared spectroscopy is to determine the identity of two compounds. The infrared region 4000 cm-1 -650 cm-1 is of great importance in studying an organic compound. Since IR spectra contain a number of bands no two compounds will have the same IR spectrum (except optical isomers). Thus IR spectra may be regarded as finger print of a molecule. 

In this technique almost all groups absorbs characteristically within a definite range. Thus a strong IR band at 1800 to 1600 cm 1 in the IR spectrum of an unknown compound indicates that a carbonyl group is present. Identical compounds have identical IR spectra. Molecules with identical or similar shapes of their IR spectra in the finger print region have the same or a similar skeleton of atoms. 

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