This may be useful reading on charge density crystallography: http://journals.iucr.org/a/issues/1998/05/00/by0157/by0157.pdf
I like the phrase ‘gourmet crystallographers’ Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark van der Woerd Sent: Thursday, February 05, 2015 9:28 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] proton scattering by X-rays Not very well. When you look in the originally quoted article, there is really not much difference in the ED for H+ and H- (which are conveniently both shown in Fig 2). You build a model that is consistent with 'book knowledge' (i.e. normal hydrogen has only one bond) and take it from there. You have a point that the resolution isn't very good at 0.89A (sorry!) but I suspect that the number of recorded reflections is much more important than the nebulous number of 0.89A (i.e. you can start to see these little details because you finally have an over-determined system parameters). What you CAN do in fact is appropriately subtract "spherical electron density" from the experimental density and see what is left (i.e. directional ED that is 'surplus'). I tried to quickly find a paper on that, they exist, and they show that experimental density does confirm what we learn in chemistry class, orbitals are not imaginary. Mark -----Original Message----- From: Doug Ohlendorf <oh...@umn.edu> To: CCP4BB <CCP4BB@JISCMAIL.AC.UK> Sent: Mon, Feb 2, 2015 11:29 am Subject: Re: [ccp4bb] proton scattering by X-rays But, how with x-rays can one experimentally tell the difference between a hydrogen and a filled orbital (say of N)? I will grant that the electron density for a bound H should extend farther from the heavy atom but I believe you would need resolution better than 0.89 Ang to see this difference. Doug Douglas H. Ohlendorf Phone: 612-624-8436 Professor FAX: 612-624-5121 Dept. of Biochemistry, Molecular Biology & Biophysics Twin Cities Campus, University of Minnesota Lab web site: <http://biosci.cbs.umn.edu/bmbb/ohlen_lab/index.html> http://biosci.cbs.umn.edu/bmbb/ohlen_lab/index.html -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK?> ] On Behalf Of Colin Nave Sent: Monday, February 02, 2015 9:04 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] proton scattering by X-rays “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 <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 <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 <mailto:peter.mo...@le.ac.uk?> > to reply directly) http://www2.le.ac.uk/departments/biochemistry/staff/moody -- 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. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
