Hi All,<br><br>I have been using the PubChem database to search for uncharged small molecules.  However, even after specifying zero charge, PubChem still outputs compounds containing amino groups (-NH2) and carboxylic acids (-COOH); since I am interested in physiological pH, these compounds would actually be charged.<br>
<br>Is there some way to exclude molecules containing these functional groups?  I&#39;ve noticed that there is an option on PubChem to include only certain atoms, but the search times out at 2 minutes if I try this.  I&#39;d like to exclude halogens and aldehydes as well, can this be specified?  Finally, after searching for numerous compounds, how could all of them be downloaded into an organized compound library?<br>
<br>If there is another online compound database besides PubChem that can be easily searched and has the same or better functionality, I&#39;d greatly appreciate any info about it.<br><br>Thanks,<br>Nancy<br><br><br><br>