Video 1 ======= Title: Exploring the database Welcome to the NASA Ames PAH IR Spectroscopic Database and this series of video tutorials. This is the first in a series of four tutorials. This one focusses on exploring the contents of the database. Our site is located at www.astrochem.org/pahdb where you enter on the main page. You start exploring by choosing either the Experimental or the Theoretical database. We will be exploring the Theoretical database here today. It has already been selected as you can see from the radio buttons. There are several ways you can search. By entering `c=50' in the search box and hitting `search' presents you with an overview of all PAHs in the database with 50 carbon atoms. The information in the overview will be discussed in the second tutorial titled ``Information in the database''. You can also Search using relaxed criteria. For example, entering `carbon eq 50' will result in the same overview. There are several Search criteria. You can also search for PAHs with a given 'charge'. By entering `c=50 charge=0', only the neutral PAHs with 50 carbon atoms are presented. Again, the relaxed criteria `c=50 neutral' will produce the same overview. For a list of the criteria, go to advanced search and explore the different drop down menus. Choosing C = 50 from the drop down menus and setting charge to neutral indeed returns the same overview. You can also explore the database more intuitively using the browse function. Hitting `Browse' presents you an overview of the PAHs present in the selected database using PAH structures as icons. Hovering over an icon will show a blow-up of the structure and clicking the blue link directs you to an overview of the information available on that PAH. The PAHs can also be viewed as a list, which shows more information per PAH. This is the end of the first tutorial. Be sure to visit the help section, `Take the tour' and read the Manual for additional information. If you have any feedback, please use the contact form under ``Help'' on the website. We hope to see you in our next tutorial titled ``Information in the database'', where we will talk about the PAH specific information available on the site. Video 2 ======= Title: Information in the database Welcome to the NASA Ames PAH IR Spectroscopic Database and this series of video tutorials. This is the second in a series of four tutorials. This one focuses on the information in the database. Our site is located at www.astrochem.org/pahdb where you enter on the main page. In the previous video tutorial you learned how to explore the contents of the database. Lets start this tutorial by finding the information that is available in the theoretical database for the PAH coronene in its neutral form. Since coronene has 24 carbon and 12 hydrogen atoms, we can search for coronene by entering `c=24 h=12 neutral' in the search box and being sure that the 'Theoretical' radio button is highlighted. Coronene is the first PAH shown in the overview after hitting enter. We read that it has uid=18, which is its unique identifier in the database. It is also possible to search for PAHs using their unique identifier. The overview is divided in three sections. Coronene's molecular structure is shown on the left. Some of coronene's structural aspects are given in the table in the center. Here you see that coronene has 12 duo hydrogens, that is, all of coronene's twelve hydrogen atoms are present as adjacent pairs on each edge ring. Solo, trio, quartet and quintet indicate other hydrogen adjacency classes and `chx' gives the number of aliphatic edge groups present. The spectrum is presented on the right as total integrated cross-section versus frequency given in wavenumbers. The chemical formula and a button labeled `Full info' are also shown. When selecting 'Full Info', three tabs appear. The first tab, labelled `Details', provides more detailed information about coronene, including the total binding energy and the computational method. Below this is the proper reference to the literature for the data shown here and the comment tells you the common name of the species you are considering if it is available. The entry under History tells you when the data was added and, if it has been updated, when that occurred. A rotatable 3D representation of coronene is to the right. This is particularly helpful in visualizing the structure for non-planar PAHs and, if present, the orientation of 3-dimensional edge groups. The next tab, `transitions', shows a Table listing the frequency, intensity and symmetry for all the fundamental vibrations. These data can also be downloaded, which we will describe in the next video tutorial titled `Selecting and downloading data'. The last tab, `zoom',again shows the spectrum of coronene, but now with the ability to zoom in on any region of interest by simply dragging the cursor across the spectrum and clicking. You can return to the full spectrum by double-clicking anywhere on the spectrum. You might have noticed that the general overview for coronene also shows a little Erlenmeyer flask. This indicates that there is a counterpart in the experimental database. You can directly compare the theoretically calculated spectrum with the experimental spectrum by clicking compare. Going back, you can obtain an overview of the experimental data by clicking the `counterpart' link. You are now in the Experimental database. The information shown is similar to that for the theoretical database, with a few exceptions. Most notably is the new `laboratory' tab. Clicking this tab presents you with the experimentally measured, baseline corrected, spectrum. This is the end of the second tutorial. Be sure to visit the help section, `Take the tour' and read the Manual for additional information. If you have any feedback, please use the contact form under ``Help'' on the website. We hope to see you in our next tutorial titled ``Selecting and downloading data'', where we will talk about selecting and downloading data. Chapter 3 ========= Title: Selecting and downloading data Welcome to the NASA Ames PAH IR Spectroscopic Database and this series of video tutorials. This is the third in a series of four tutorials. This one focusses on selecting PAHs and downloading their spectra. Our site is located at www.astrochem.org/pahdb where you enter on the main page. In the previous video tutorial we looked at the information on coronene in the both the theoretical and experimental databases. Lets start by again pulling up coronene's information from the theoretical database. This time we will use coronene's unique identifier, which is 18. The information in the overview screen has been described in the second video tutorial titled ``Information in the database''. One thing we didn't mention is the `select' link. Clicking 'select' will highlight the chemical formula and update the counter above `Selection' which indicates the number of PAHs currently under consideration. Clicking `Selection' takes you to an overview of the PAHs currently selected. In this example four PAHs have now been selected, all related to coronene. You can switch to icon view using the layout buttons. To focus on coronene, we deselect the iron containing PAH leaving coronene in its neutral and singly charged states selected. To obtain spectroscopic data for these PAHs, you click on `Download'. You can choose to download only the data you have previously selected or to download the entire experimental or theoretical database. After providing your e-mail address, name, company and agreeing to cite the proper references when using these data, you will be sent a link that allows you to download the available data in XML data format. These data include detailed information on the PAHs such as weight, total binding energy, etc, as well as the geometric data and, of course, the spectroscopic data. You will need a parser to read these data into your favorite data analysis program. Or, if you are an IDL user, you can download the IDL-suite provided on the site using the link on the ``Download'' page. This will be described further in the next tutorial, entitled 'Tools'. If you are only interested in downloading the spectroscopic data, you can download those from the information overview. You can access that by clicking `Selection' and then `Full info'. Clicking the tab labelled `Transitions' offers you the possibility to download the spectroscopic data in both XML and ASCII data format. For PAH's in the experimental database, you can download the spectroscopic data from the `Transitions' tab in the same way. If available, you can download the laboratory spectrum in ASCII format from the tab labelled `Laboratory'. This is the end of the third tutorial. Be sure to visit the help section, `Take the tour' and read the Manual for additional information. If you have any feedback, please use the contact form under ``Help'' on the website. We hope to see you in our next tutorial titled ``Tools'', where we will talk about the available tools to work with the spectroscopic data both online and offline. Video 4 ======= Title: Tools Welcome to the NASA Ames PAH IR Spectroscopic Database and this series of video tutorials. This is the fourth and last in a series of four tutorials. This one focusses on the tools available which allow you to work with the spectroscopic data in the database. Our site is located at www.astrochem.org/pahdb where you enter on the main page. In the previous tutorial titled ``Selecting and downloading data'', you learned how to select and download data. Lets start by selecting again coronene in its neutral and singly charged states from the theoretical database. We will do this by entering ``c=24 h=12'' in the search box and choosing the icon layout. The available tools are found under `Tools'. Currently three tools are available. 1) a tool to co-add spectra, 2) a tool to compare spectra in a stack plot and 3) a tool to compare the spectrum of a single PAH at different emission temperatures using a stack plot. All these tools take the spectral data from the PAHs you have selected and convolves the integrated cross-sections with Lorentzian band shapes. In `General settings' you can specify the parameters for the Lorentzian band shapes and the spectroscopic region of interest. For this example we select a wavelength range from 2.5 to 20 micron and the applied Lorentzian band shapes will be given a full-with-at-half-maximum of 10 wavenumbers. Unless you specify an emission temperature, you will obtain an absorption spectrum at about 0 Kelvin. A blackbody function is used to approximate an emitting PAH the at the provided temperature. Here we will not make use this function, by not ticking the relevant box. The three selected coronenes can now be co-added by hitting `Go!' under `Co-add'. We wait a few seconds and the co-added spectrum appears and the badge above `Results' is updated. The result is numbered so you can keep track of your different results. Also shown are links to the details on the individual species. You can choose to download the graph as a Postscript file by pressing `Download PostScript'. All your results will be stored under `Results' so you may compare them at a later stage. Returning to `Tools' you can now compare each spectrum to one-another by hitting `Go!' under `Stack'. The result is added to `Results'. Each panel shows the chemical formula and the structure of the molecule with the spectrum for reference. Again, links to the overviews of the individual PAHs are shown and the graph can also be downloaded as Postscript. Your previous result from the co-add has been automatically `Collapsed' to allow you to focus on the latest result. Pressing the `Expand' link will expand the co-add again. Returning one last time to the `Tools', the spectrum of a single PAH at different emission temperatures can be compared under `Temperature Stack'. First you need to specify the PAH from your selection you want to compare. Here we choose singly, positively charged coronene from the drop-down menu and lets enter five temperatures, 500, 600, 700, 800 and 1000 Kelvin. After hitting `Go!' the result is added to `Results'. Each panel displays the emission temperature for reference. A link to the overview of the PAH is shown and the graph can again be downloaded as Postscript This is the end of this tutorial series. Be sure to visit the help section, `Take the tour' and read the Manual for additional information. If you have any feedback, please use the contact form under ``Help'' on the website.