Tim Well if you google for proton scattering by x-rays, the most relevant thing you find are these emails! d=0.26A would be well within the limit for a silver source. Most charge density studies seem to be around d=0.5A - 0.7A, including the crambin studies. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC16211/ At these resolutions, the form factor for atoms break down and one has to include multipoles around the atoms to describe the bonds - the point of doing this. The proton itself will also have a Debye Waller factor, weakening its contribution
However, for an isolated hydrogen atom (at 0 kelvin), as an intellectual exercise, I think your analysis is correct. The next question is, if adopting a modified form factor, whether the proton scattering acts coherently with the electron scattering (i.e. sum then square) or incoherently (square then sum). Also how does one handle the opposite charges when doing this? Perhaps one should let this rest! Colin -----Original Message----- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: 03 February 2015 22:57 To: Nave, Colin (DLSLtd,RAL,LSCI); ccp4bb Subject: Re: [ccp4bb] proton scattering by X-rays Hi Colin, I understood the jest, of course. Now I got curious: At 2theta=0, the scattering from H is 1e, so I assume the the scattering length for its nucleus is 1e/1860 = 0.00054. According to the data from Phil Coppens web site, the atomic scattering factor for H reaches this value at sin theta / lambda = 1.95, i.e. d=0.26A. That's far away from the wavelength 'we' use, but not too far off from the resolution limit on a Silver source (0.31A), is it? I am not sure this can be totally neglected. Am I wrong? Cheers, Tim On 02/03/2015 04:03 PM, Colin Nave wrote: > Hi Tim > Although my SHELX comment was in jest, your point illustrates the programs > versatility. You are also right about the flat(ish) form factor for the > proton. > To get to a resolution where there is a cross over would require a very short > wavelength. Other processes would then dominate. A nice source for this is > the x-ray data booklet from LBL, in particular the chapter on scattering of > x-rays from electrons and atoms. > http://xdb.lbl.gov/Section3/Sec_3-1.html > Interestingly fig 3-1 in this does not include coherent scattering from > nuclei presumably because it is negligible compared with the other processes > - in practice Ian was correct in saying that a proton is effectively > invisible to x-rays of the energy we usually use. > > Colin > > > -----Original Message----- > From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] > Sent: 02 February 2015 22:08 > To: Nave, Colin (DLSLtd,RAL,LSCI); ccp4bb > Subject: Re: [ccp4bb] proton scattering by X-rays > > Hi Colin, > > you can add f' for every atom type in SHELXL yourself, so in that sense, it > has been incorporated in SHELX. Bear in mind that the nucleus is point-like > to X-rays at ordinary wavelengths so that it should not have a form factor > like the electron cloud but a constant scattering length - just as they do > for neutron scattering. > > You can do the maths at what resolution the form factor and the > constant > 1:1860 scattering length contribution cross. It is not ridiculously small but > nowhere near 0.8A. Charge density people may need to take this into account, > but I don't know if they do. > > Cheers, > Tim > > On 02/02/2015 04:03 PM, Colin Nave wrote: >> “As you say the proton itself is invisible to X-rays.” >> Not quite! The ratio of scattering between electrons and protons should go >> as the inverse square of the masses. >> Ratio of mass 1:1860, ratio of scattering 1:3459600. A small correction but >> doubtless it has been incorporated in to SHELX. >> Colin >> >> >> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of >> Ian Tickle >> Sent: 02 February 2015 13:35 >> To: ccp4bb >> Subject: Re: [ccp4bb] proton scattering by X-rays >> >> >> Peter, if it's a covalently-bonded H atom it surely can't be a bare proton, >> it must have at least some partial electron around it for the (possibly >> partial) covalent bond, enough to diffract X-rays anyway. As you say the >> proton itself is invisible to X-rays. >> Cheers >> -- Ian >> >> On 2 February 2015 at 13:08, Peter Moody >> <pcem1bigfi...@gmail.com<mailto:pcem1bigfi...@gmail.com>> wrote: >> 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<mailto:peter.mo...@le.ac.uk> to >> reply >> directly) >> >> http://www2.le.ac.uk/departments/biochemistry/staff/moody >> >> >> > > -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. 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