Re: [ccp4bb] proton scattering by X-rays
Dear Jacob, there was a nice small computation project by Anne Bochow published in the CCP4 Newsletters (2005), http://www.ccp4.ac.uk/newsletters/newsletter42/content.html, communication 9, illustrating how strong and how confusing the ripples may be indeed; if you want I may send it you off list the corresponding pdf file. Please make a look the figures, they are very impressive. And Pavel just commented how to distinguish such the ripples from the peaks for the deformation bond density. With best regards, Sacha Urzhumtsev De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Keller, Jacob [kell...@janelia.hhmi.org] Envoyé : jeudi 5 février 2015 21:53 À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] proton scattering by X-rays What about the bogey of Fourier truncation ripples--I have heard many have been fooled by the into thinking they were seeing orbitals. How does one tell the difference? JPK
Re: [ccp4bb] proton scattering by X-rays
> What about the bogey of Fourier truncation ripples--I have heard many have > been fooled by the into thinking they were seeing orbitals. How does one > tell the difference? Indeed, there are such dangers. Hints are here: On the possibility of observation of valence electron density for individual bonds in proteins in conventional difference maps. (2004). Acta Cryst., D60, 260-274. Have a look at Figure 4. Then compare with Figure 1 here: J. Biol. Chem. (1999) 274, 20753-29755. Bottom line is: be careful with unbalanced Fourier syntheses, balanced ones may be a safer option. Pavel
Re: [ccp4bb] proton scattering by X-rays
What about the bogey of Fourier truncation ripples--I have heard many have been fooled by the into thinking they were seeing orbitals. How does one tell the difference? JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Jeffrey Sent: Thursday, February 05, 2015 3:52 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] proton scattering by X-rays Mark, In the small-molecule crystal structures I work with it's relatively common to see localized difference electron density along covalent bonds or in the places you'd expect to see lone pairs during refinement after you've fit and modeled the atoms reasonably well and the phases are pretty good. It's usually not as strong as difference density for hydrogens, before you put them in, but it's often pretty clearly visible once you have. (I use SHELXLE as an interface for small molecule refinements because of a somewhat Coot-like experience in viewing maps). Phil Jeffrey Princeton > 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
Re: [ccp4bb] proton scattering by X-rays
Mark, In the small-molecule crystal structures I work with it's relatively common to see localized difference electron density along covalent bonds or in the places you'd expect to see lone pairs during refinement after you've fit and modeled the atoms reasonably well and the phases are pretty good. It's usually not as strong as difference density for hydrogens, before you put them in, but it's often pretty clearly visible once you have. (I use SHELXLE as an interface for small molecule refinements because of a somewhat Coot-like experience in viewing maps). Phil Jeffrey Princeton 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
Re: [ccp4bb] proton scattering by X-rays
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 To: CCP4BB 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 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 ar
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 To: CCP4BB 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 -Original Message- From: CCP4 bulletin board [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] 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 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 -- 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
Re: [ccp4bb] proton scattering by X-rays
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 To: CCP4BB 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
Re: [ccp4bb] proton scattering by X-rays
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 >> 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-a
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 >> 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 signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] proton scattering by X-rays
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 > 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 -- 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
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 > 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 signature.asc Description: OpenPGP digital signature
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 -Original Message- From: CCP4 bulletin board [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] 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 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 -- 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
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] 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 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 -- 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
Re: [ccp4bb] proton scattering by X-rays
Thank you all for explaining, I'm glad it was my pedantic lack of ability to get over the description and think of the chemistry that was the problem. Of course the positive charge would not be localised just on the hydrogen, it is not really just a proton and so it will have some electron density. Peter On 2 February 2015 at 13:08, Peter Moody 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 to reply directly) > > http://www2.le.ac.uk/departments/biochemistry/staff/moody > >
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 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 to reply directly) > > http://www2.le.ac.uk/departments/biochemistry/staff/moody > >
Re: [ccp4bb] proton scattering by X-rays
Hi Peter, I don't have access to the paper from here, but the abstract implies that the H+ is attached to a cysteine sulphur. In that case it have the shared electrons to scatter X-rays. The text "a proton (H+) attached to the sulphur of a cysteine ligand" is not very pretty. I would call it a hydrogen atom in this context, or I would at least leave out the '(H+)'. Perhaps the full paper is clearer. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of > Peter Moody > Sent: Monday, February 02, 2015 14:08 > To: CCP4BB@JISCMAIL.AC.UK > 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.ht > ml?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 >
