Bond lengths in organic and metal-organic compounds revisited:X—H bond lengths from neutron diffraction data

Abstract

The number of structures in the Cambridge Structural Database (CSD) has increased by an order of magnitude since the preparation of two major compilations of standard bond lengths in mid-1985. It is now of interest to examine whether this huge increase in data availability has implications for the mean bond-length values published in the late 1980s. Those compilations reported mean X-H bond lengths derived from rather sparse information and for rather few chemical environments. During the intervening years, the number of neutron studies has also increased, although only by a factor of around 2.25, permitting a new analysis of X-H bond-length distributions for (a) organic X = C, N, O, B, and (b) a variety of terminal and homometallic bridging transition metal hydrides. New mean values are reported here and are compared with earlier results. These new overall means are also complemented by an analysis of X-H distances at lower temperatures (T < or = 140 K), which indicates the general level of librational effects in X-H systems. The study also extends the range of chemical environments for which statistically acceptable mean X-H bond lengths can be obtained, although values from individual structures are also collated to further extend the chemical range of this compilation. Updated default 'neutron-normalization' distances for use in hydrogen-bond and deformation-density studies are also proposed for C-H, N-H and O-H, and the low-temperature analysis provides specific values for certain chemical environments and hybridization states of X.

Hirshfeld Atom Refinement

“…The N-H amide distances from both experiments are shorter by $0.02-0.03 Å than the N-H ammonium distances at all temperatures. This is in agreement with the average neutron reference values (Allen & Bruno, 2010). The distinction of the C-H distances is a bit less clear,…”

“…For hexahydro-1,3,5-trinitro-1,3,5-triazine, the average of six methylene C-H bond distances was found to be 1.073 (12) Å at 20 K and 1.082 (15) Å at 298 K, to be compared with the corresponding room-temperature neutron result of 1.082 (12) Å (Choi & Prince, 1972) and the average methylene C-H neutron distances of 1.097 (10) Å at T 60 K and 1.087 (16) Å at T ! 240 K (Allen & Bruno, 2010). For the ferroelectric croconic acid (Zhurov & Pinkerton, 2013) the average of the two O-H distances is 0.941 Å , to be compared with an average neutron value for C ar O-H groups of 0.992 (17) Å (Allen & Bruno, 2010).…”

NMR characterisation of dynamics in solvates and desolvates of formoterol fumarate

“…Figure 7 plots the measured spin-lattice relaxation rate as a function of inverse temperature, and compares this with a curve showing relaxation rates calculated on the basis of dipolar relaxation using the motional model and fitted parameters obtained from analysis of the 2 H relaxation data, i.e. rotational diffusion on a cone with cone half-angle 10.6 The value of the 13 C, 1 H dipolar coupling used was 24 kHz (corresponding to a distance of 1.08 Å [36]). Given the absence of fitting parameters, the match between calculated and experimental data is excellent.…”

The active site of hen egg-white lysozyme: flexibility and chemical bonding

“…Subsequently, C-H, N-H and O-H bonds were elongated towards the bond-length values known from neutron diffraction (Allen & Bruno, 2010). This procedure is necessary to counteract the known shortening of bond lengths for attached H atoms arising from the shift of the one-electron entity, as observable by X-ray diffraction, away from the true position of the hydrogen nucleus.…”