It totally depends on what you define as your C-H bond length. For XRD work, the C-H is the distance between the electron center-of-masses. For neutron or high-resolution XRD work, you can determine the distance between the nuclear center-of-masses. They are different by about 0.1A. The electron COM for hydrogen is substantially shifted along the bond towards the carbon atom.
I did a very precise determination of 1,1-dicyclobutanedicarboxylic acid at 20K, and the C-H bond lengths averaged to 0.991A, and far shorter than the 1.096A you'd expect from a neutron diffraction study. The VDW distances shouldn't be that important since the potential isn't that sensitive with a difference of 0.1A. If you have to restrain C-H distances for XRD refinement, then they should be shortened. BDS On Sat, April 29, 2017 8:22 am, benjamin bax wrote: > > > > 'Most distances between bonded atoms were settled long ago > to high accuracy, but, in the case of > hydrogens, the values in common use often differ by > as much as 20%.' > > Phenix / MolProbity Hydrogen Parameter Update > > Deis, L. N., Verma, V., Videau, L. L., Prisant, M. G., Moriarty, N. W., > > Headd, J. J., Chen, V. B., Adams, P. D., Snoeyink, J., Richardson, J. S. & > Richardson, D. C. (2013). Comput. Crystallogr. Newsl. 4, 9â10. > > > > On 28 Apr 2017, at 18:33, Bernhard Rupp <hofkristall...@gmail.com> wrote: > > Dear Fellows of the Bond, > > when validating a QM refined homology model with Molprobity, I noticed > various 8 sigma deviations in the carbon-hydrogen bond distances. > Out of curiosity, I then used refmac to calculate riding Hs for the same > model, and at least in one instance (N-H backbone) there are > significant differences between Molprobity and Refmac H bond distances > (differences to the QM distances in other > instances I find interesting, but less relevant for us). > > The riding H vs Molprobity presumably should be consistent, because if we > use them in VDW restraints but > they differ from the validation target, systematic bias will occur. I have > no feel how significant that effect > might be â maybe someone more erudite can comment. > > Examples > > distance MP REF QM > backbone N-H 0.86 1.01 1.00 > phenyl C-H 0.93 0.93 1.09 > > Best, BR > > PS: If someone has accurate experimental values for CH distances Iâd > appreciate a link. > No access to CSD. > > ------------------------------------------------------ > Bernhard Rupp > Crystallographiae Vindicis Militum Ordo > http://www.hofkristallamt.org/ <http://www.hofkristallamt.org/> > b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> > +1 925 209 7429 > +43 767 571 0536 > ------------------------------------------------------ > Many plausible ideas vanish > at the presence of thought > ------------------------------------------------------ > > > Dr Ben Bax > > York Structural Biology Laboratory, > Department of Chemistry, > University of York, > York YO10 5DD > > ben.d.v....@gmail.com > > > > > > -- Bernard D. Santarsiero Associate Director, UI Health Systems Biorepository Research Professor Center for Biomolecular Sciences and the Department of Medicinal Chemistry and Pharmacognosy Center for Structural Biology Center for Clinical and Translational Science University of Illinois at Chicago MC870 3070MBRB 900 South Ashland Avenue Chicago, IL 60607-7173 USA (312) 413-0339 (office) (312) 413-9303 (FAX) http://www.uic.edu/labs/bds http://scholar.google.com/citations?user=fGauLBMAAAAJ
