Hi Peter, Try to think of it as a quantum chemist: What you call H+ is not "H+ floating in space". They are hydrogens bound to the rest of the structure by means of electrons. These electrons can be described by wave functions, which relate to probabilities where they (electrons) might be.
If we consider for simplicity water, we learn in a simple model that each O-H bond contains two electrons. On average, they "like to be" closer to O and than to H. But it does not mean "H has none". You need high-quality, high-resolution data to actually visualize this and in small molecule work this is commonly done. In macromolecular work not so much, but my search easily found an example (see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC16211/ for Crambin) where you can "see" the electrons between N and H in the backbone. The main difference between what you think of as H+ and H- is one and two bonds, respectively. The density in their figures does not look all that different, but says "something should be here". We then propose H in the location and show that it adequately explains the experimental data. HTH Mark -----Original Message----- From: Peter Moody <pcem1bigfi...@gmail.com> To: CCP4BB <CCP4BB@JISCMAIL.AC.UK> Sent: Mon, Feb 2, 2015 11:33 am Subject: [ccp4bb] proton scattering by X-rays Dear BB I have (again) realised how limited by understanding of our subject is. In Nature’s online site http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14110.html?WT.ec_id=NATURE-20150129 there is a paper describing an X-ray structure determined with sub-atomic data (nice!). The figures show density for H+ as well as H-. In my simple way I had assumed that any X-ray scattering from the nucleus was negligible, and that the electrons are responsible for this. I would expect a proton (i.e. H+) alone to be invisible to X-rays, and certainly not to look similar to a hydride (with two electrons in (electron density) maps. What have I missed? Could someone please explain, or point me to a suitable reference? Best wishes, Peter (please use peter.mo...@le.ac.uk to reply directly) http://www2.le.ac.uk/departments/biochemistry/staff/moody
