Hi everyone, Prompted by this discussion I ran a series of CSD conquest searches for peroxide in various environments. CSD conquest makes it easy to perform fairly complex searches (and was used for the Engh & Huber amino acid restraint library for amino acids still extensively used today).
Searching for isolated hydrogen peroxide H2O2 results in 66 CSD entries as hits There are 87 oxygen-oxygen distances with a mean value 1.454Å and a standard deviation 0.022Å So the CCP4 monomer library entry for hydrogen peroxide H2O2 PEO.cif with a distance of 1.461Å and an esd 0.012Å is good. Using conquest to search for a singly charge hydrogen peroxide ion HO2- that is bound to any metal atom (M-O-O-H) results in 17 CSD hits, There are 27 oxygen-oxygen distances with a mean value 1.473Å and a standard deviation 0.060Å There is no PDB component or CCP4 monomer for a singly charged hydrogen peroxide ion. Using conquest to search for a doubly charged peroxide ion O2- that is bound to any metal atom (M-O-O) results in only 3 CSD CSD hits, The 3 O-O distances are: | CSD entry | coordinated to. | distance | | ETBSCB <https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=ETBSCB> | Co cobalt | 1.348Å | | EWOPEM <https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=EWOPEM> | Pd palladium ion. | 1.293Å | | NUNJOX <https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=NUNJOX> | Co cobalt ion. | 1.301Å | So the oxygen-oxygen distance for doubly charged peroxide ions that coordinate metals is shorter than isolate hydrogen peroxide Or the more normal singly charged peroxide ion with one hydrogen atom. Your observed distance of 1.15Å would seem to be consistent with a doubly charged peroxide coordinated to a metal ion, Particularly after Boaz’s comment. There is a PDB component and CCP4 monomer library entry for a doubly charged peroxide ion O2- PER * The current CCP4 8.0 monomer library uses a O-O distance 1.150 ± 0.020Å * Global Phasing Grade2 uses a O-O distance 1.316 ± 0.030Å based on the UFF force field. Looking a PDB entries with PER modelled it is normally not next to a metal atom. I think it is unlikely that these would be doubly negatively charged so using PER would likely lead to unrealistic short O-O distances. Most hydrogen peroxide ions are likely to be hydrogenperoxide(1-) https://pubchem.ncbi.nlm.nih.gov/compound/18500 <https://pubchem.ncbi.nlm.nih.gov/compound/18500> Perhaps there could be a new PDB component for this species? Otherwise it would be a much better idea to model the molecules as PEO Hope this helps, Oliver p.s. I think that it is a great idea for restraint dictionary to include information as to the source of a parameter so Global Phasing Grade2 https://www.globalphasing.com/buster/manual/grade2/manual/introduction.html <https://www.globalphasing.com/buster/manual/grade2/manual/introduction.html> includes information as to the source of restraints for instance for PER: # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.aromatic _chem_comp_bond.value_dist_nucleus _chem_comp_bond.value_dist_nucleus_esd _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd _chem_comp_bond.source_value_dist_nucleus _chem_comp_bond.source_value_dist_nucleus_esd _chem_comp_bond.source_value_dist _chem_comp_bond.source_value_dist_esd PEO O1 O2 single n 1.444 0.069 1.444 0.069 Mogul_mean_118_hits Mogul_sd Mogul_mean_118_hits Mogul_sd PEO O1 HO1 single n 0.972 0.020 0.850 0.020 MMFF94s_equilibrium default_to_H ecloud ecloud PEO O2 HO2 single n 0.972 0.020 0.850 0.020 MMFF94s_equilibrium default_to_H ecloud ecloud # So you can see that the O1-O2 distance is based on Mogul results. This makes tracking down information easier. > On 29 Nov 2022, at 07:01, [email protected] > <[email protected]> wrote: > > Dear Boaz, > > You're quite right, in my haste to reply last night I only related part of > the discussion relating to peroxide. In a bid to identify the diatomic > ligand, which appears on oxygen exposure, I quoted the peroxide bond length > as being too long, then went on to say it is much more like dioxygen in > oxyhaemoglobin/myoglobin and referenced structures from yourself and Simon > Phillips. > > Best wishes, > Steve > > > Dr Stephen Carr > Research Complex at Harwell (RCaH) > Rutherford Appleton Laboratory > Harwell Oxford > Didcot > Oxon OX11 0FA > United Kingdom > Email [email protected] <mailto:[email protected]> > tel 01235 567717 > From: Boaz Shaanan <[email protected] <mailto:[email protected]>> > Sent: 28 November 2022 23:33 > To: Carr, Stephen (MRC,RAL,RCAH) <[email protected] > <mailto:[email protected]>> > Subject: Re: [ccp4bb] Question about CCP4 monomer dictionaries > > Hi stephen, > > I obviously don't have the full context of your case, but I am not sure why > you invoked peroxide as a reference for the O-O bond length in the context of > oxygen-metal complex. In my good old oxy haemoglobin structure (1HHO) the O-O > bond length in Fe-O-O is 1.22 A. It's also worth checking MbO2 with Fe and > various metals which are most likely higher resolution structures. > > I could of course be completely wrong line of thought. > > Cheers, > > Boaz > > > > Boaz Shaanan, Ph.D. > Dept. of Life Sciences > Ben-Gurion University of the Negev > Beer-Sheva 84105 > Israel > > E-mail: [email protected] <mailto:[email protected]> > Phone: 972-8-647-2220 > Fax: 972-8-647-2992 or 972-8-646-1710 > > > > > From: CCP4 bulletin board <[email protected] > <mailto:[email protected]>> on behalf of [email protected] > <mailto:[email protected]> > <[email protected] > <mailto:[email protected]>> > Sent: Monday, November 28, 2022 10:03 PM > To: [email protected] <mailto:[email protected]> > <[email protected] <mailto:[email protected]>> > Subject: Re: [ccp4bb] Question about CCP4 monomer dictionaries > > Dear BB, > > Thank you for all the helpful responses. To give a bit more context to my > question, I have a 1.2 A structure with a diatomic ligand bound to a metal at > the active site, which we believe is an oxygen species. The bond length is > 1.22 A and I made a comment in the discussion that this was unlikely to be a > peroxide species as the bond length was shorter than the 1.48 A typically > observed. The referee has questioned the validity of the 1.48 A, which led > to my original question. > > Best wishes, > Steve > > PS I have tried Raman spectroscopy with no definitive result. > > Dr Stephen Carr > Research Complex at Harwell (RCaH) > Rutherford Appleton Laboratory > Harwell Oxford > Didcot > Oxon OX11 0FA > United Kingdom > Email [email protected] <mailto:[email protected]> > tel 01235 567717 > From: Paul Emsley <[email protected] > <mailto:[email protected]>> > Sent: 28 November 2022 19:20 > To: Carr, Stephen (MRC,RAL,RCAH) <[email protected] > <mailto:[email protected]>> > Subject: Re: [ccp4bb] Question about CCP4 monomer dictionaries > > > On 28/11/2022 17:29, [email protected] > <mailto:[email protected]> wrote: >> Dear CCPBB, >> >> I have a question regarding the origin of the monomer libraries in CCP4. I >> ask because I have quoted the bond length listed in the monomer library >> describing peroxide in a manuscript and a referee has asked for a reference >> since they seem to disagree with the quoted value of ~1.48 A. My >> understanding is that parameters describing bond length, angles etc are >> derived from structures in the CSD is this the case? Is there an >> appropriate reference out there somewhere? >> > > When you say "peroxide," I presume that you mean H2O2. The entry for > that in the monomer library is PEO. The bond length between the oxygen > atoms in PEO is 1.461A. Perhaps your referee is thinking of the > peroxide ion, which indeed would have a different bond length (1.15). > Both PEO and PER would, to my mind, be susceptible to radiation damage, > so one wonders what is actually in the crystal. To address question, one > would make an "Fearly-Flate" map. > > One can (in principle) dig into the Acedrg table of bond lengths to examine > how many > examples, of this sort of chemistry exist (I did it a few years ago), but I > don't recall > now how to do it for this example. > > Regards, > Paul. > > > This email and any attachments may contain confidential, copyrightand or > privileged material, and are for the use of the intended addressee only. 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