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<HTML> <HEAD> <meta http-equiv="Content-Language" content="en-us"> <TITLE>Chemcraft - compute mean absolute deviation tool</TITLE> <meta name="Description" CONTENT="A convenient graphical program for working with quantum chemistry calculations. Provides visualization of Gamess/Gaussian output files, useful utilities for preparing new jobs for calculation."> </HEAD> <BODY BGCOLOR=#F3F3F3> <div align="center"> <TABLE WIDTH=679 BORDER=1 CELLPADDING=0 CELLSPACING=0 bordercolor="#FFFFFF" bgcolor="#FFFFFF"> <TR> <TD height="204" bordercolor="#808080"> <IMG SRC="images/molecule.jpg" width=123 height=200></TD> <TD height="131" bordercolor="#808080"> <IMG SRC="images/title.jpg" width=427 height=129 align="bottom"> </TD> </TR> <TR> <TD colspan="2" height="405" valign="top" width="677"> <h2 style="mso-layout-grid-align:none;text-autospace:none" align="left">Mass spectrum calculator</h2>     The menu items "Mass spectrum analysis tools" can be useful for chemists dealing with mass spectra:   Tools/Mass spectrum analysis tools/Calculate the mass of current molecule with standard distribution of isotopes   This utility simply computes the mass of your molecule. You can edit the table with the standard masses of isotopes and their percentages via "Check source data on atomic masses". By default, the file "atomicmasses.txt" in Chemcraft folder is read; this file was generated at NIST Chemistry WebBook site.   Tools/Mass spectrum analysis tools/Calculate the mass of current molecule with custom distribution of isotopes   With this option, you can specify the isotopes for your molecule.   By default, all isotopes are taken for the computation with standard percentages and masses. If you click on an element of the check box list in this window, the program will uncheck other isotopes for this atom. This means that for each atom, either all isotopes are taken with standard percentages, or only one isotope is taken with percentage 100%.   Consider you have a CH molecule. The C atom has two isotopes: C12 with m=12.0 and percentage 98.93%, C13 and with m=13.00335 and percentage 1.07%. The H atom has two isotopes: H1 with m=1.00782 and percentage 99.99%, H2 with m=2.0141 and percentage 0.01%. By default (when all checkboxes are checked), the total mass is computed as follows: M=12.0*0.9893+13.00335*0.0107+1.00782*0.9999+2.0141*0.0001=13.0187. If you check the 2H checkbox, the sum will be computed as follows: M=12.0*0.9893+13.00335*0.0107+2.0141*1=14.0248 Checking the checkboxes in this form does not alter the table of standard isotope masses and percentages for the form below.   Tools/Mass spectrum analysis tools/Calculate the mass spectrum of fragment ions    This utility can compute the peak in mass spectrum of a molecular or fragment ion, with standard isotope masses and percentages (if you want to alter these data, the file "atomicmasses.txt" with them can be edited manually in any text editor).   If the checkbox "Set custom molecular formula" is pressed, you can manually set the molecular formula of your compound; however, with this option, the tools for checking rearrangement ions will not be available, since these tools need not only the molecular formula but also the molecular structure (more exactly, the information about the bonds between atoms).   If the combo box "Compute the mass spectrum of the molecular ion" is chosen, after pressing "Calculate" the program simply computes the mass corresponding to specified molecule. After pressing this button, you can click on the first line in the list at the center of the window, and then press "Show the mass spectrum of selected fragment ion" and the program will draw a mass spectrum (more exactly, the form of the peak of the molecular ion). The textbox "Broadening" should have the value corresponding to the resolution of your mass spectrometer.   If the combo box "Compute the mass spectrum of all fragment ions" is checked, after pressing "Calculate" the program will show a list of all possible fragment ions which correspond to the specified molecular formula.    By default, the combo box "No filter" is set which means that all combinations of atoms below the molecular formula can be got (for example, if the molecular formula if CH2, the program will show a list of ions CH2, CH, C, H2, H). If the combo box "Exclude rearrangement ions" is checked, the program will use the information about the bonds in your molecule, and no rearrangement ions will be shown in the list (e.g. for the methane molecule CH4, the ions H4, H3, H2 will not be shown). For big molecules, this option will work too slowly.   If the combo box "Recombine ions after bond removal" is checked, the algorith of ions enumeration will work as follows. The program will remove arbitrary bonds in your molecule (by default - all triples of bonds which are single), and check what fragments appear, and then recombine these fragments. Consider you have this molecule:  <img border="0" src="images/massspecrecomb1.jpg" width="452" height="277">   When the program removes the bonds the bonds C1-C11 and C17-C21, the following recombination ions will be possible: <img border="0" src="images/massspecrecomb2.jpg" width="248" height="179">  <img border="0" src="images/massspecrecomb3.jpg" width="263" height="234"> <img border="0" src="images/massspecrecomb4.jpg" width="217" height="180"> <img border="0" src="images/massspecrecomb5.jpg" width="442" height="254"> <img border="0" src="images/massspecrecomb6.jpg" width="355" height="262"> <img border="0" src="images/massspecrecomb7.jpg" width="385" height="330">     The last 3 fragments will be checked only if you set the option "Customize bonds removal options/Recombine fragments". Note that if your molecule contains aromatic cycles, you should set the auto-determination of aromatic bonds via "Tools/Chemcraft incorrectly identifies bonds in your molecule?/Identify bond types by atom valence information (aromatic bonds)". Possibly you should also switch on the "Display/Quick" display scheme since this scheme shows whether a bond is single or aromatic or double: <img border="0" src="images/massspec_arom_doublebonds_correct_incorrect.png"> You can also set the bonds in your molecule manually for your purposes. These options are useful since Chemcraft allows to specify the maximum number of single bonds which will be removed by the fragments enumerator, and the maximum number of non-single bonds (aromatic, double, triple...). For aromatic cycles, often it is better to specify the limit of non-single bonds to be removed to 1, which means that the aromatic cycles can't be broken during the ionization in the mass spectrometer.   If the combo box "Find possible fragment ions of the specified molecule which can produce the specified peak" is checked, the fragments enumerator will also check whether each found fragment ion produces a peak in the range specified at the "Peak position..." textboxes (otherwise this fragment will not be added to the list).   You can view an image of a found fragment via the button "Show the image of the selected fragment ion".        <a href="/help.html">BACK</a>   </TD> </TR> <TR> <TD colspan="2" height="405" valign="top" width="677">   </TD> </TR> </TABLE> </DIV> </BODY> </HTML>