non-H Atoms (non-h + atom)

Distribution by Scientific Domains

Selected Abstracts

The protein content in crystals and packing coefficients in different space groups

Klas M. Andersson
A precise way of estimating the packing coefficient, i.e. the ratio between the protein and unit-cell volume, or solvent content in protein crystals is given. At present, the solvent content is not given for most proteins in the Protein Data Bank and in many cases where it is given the values are dubious. The mean density of proteins in the crystalline form is around 1.22,g,cm,3, not 1.35,g,cm,3 as usually stated. This is equivalent to 19.5,Å3 per non-H atom. A statistical investigation of the average protein content and packing coefficient in different space groups is presented. The packing coefficients are generally higher in the most frequently occurring space groups than in the uncommon space groups. There is also a remarkable difference in frequency distribution for enantiomorphous pairs of space groups. [source]

Towards the best model for H atoms in experimental charge-density refinement

Anna A. Hoser
The consequences of different treatments of H atoms in experimental charge-density studies are discussed. Geometric and topological parameters obtained after applying four different H-atom models in multipolar refinement on high-resolution X-ray data only were compared with the results obtained for a reference joint high-resolution X-ray/neutron refinement. The geometry and the topological critical point and integrated parameters closest to the reference values were obtained after a mixed refinement (high-order refinement of heavy atoms, low-angle refinement of H atoms and elongation of the X,H distance to the average neutron bond lengths) supplemented by an estimation of the anisotropic thermal motions of H atoms using the SHADE program. Such a procedure works very well even for strong hydrogen bonds. The worst fit to the reference results for both critical point and integrated parameters was obtained when only the standardization to the average neutron X,H distances was applied. The non-H-atom parameters are also systematically influenced by the H-atom modeling. In order to compare topological and integrated properties calculated for H and non-H atoms in multipolar refinement when there are no neutron data, the same treatment of H atoms (ideally the mixed refinement + estimated anisotropic atomic displacement parameters for H atoms) should be applied. [source]

Convergence study of a Schrödinger-equation algorithm and structure-factor determination from the wavefunction

Kostas Bethanis
The algorithm [Bethanis, Tzamalis, Hountas & Tsoucaris (2002). Acta Cryst. A58, 265,269] which reformulates the quantum-mechanical problem of solving a Schrödinger (S) equation in a crystallographic context has been upgraded and tested for many aspects of convergence. The upgraded algorithm in reciprocal space aims at determining a wavefunction ,H such that (a) ,H fulfils the S equation within certain precision and (b) ,H minimizes by least squares the differences between the calculated structure factors from the wavefunction and the observed ones. Calculations have been made with three molecules (11, 41 and 110 non-H atoms in the asymmetric unit) for different numbers of initially given phases. Three main questions have been addressed: (I) Does the iterative calculation of the wavefunction converge? (II) Do the calculated wavefunctions converge to a unique set of ,H values independent of the initial random set of ,H? (III) Is the calculated ,H set a good approximation of a wavefunction able to produce within certain errors the correct values of the phases of the structure factors? Concerning questions (I) and (II), our results give a strong hint about fast convergence to a unique wavefunction independent of the arbitrary starting wavefunction. This is an essential prerequisite for practical applications. For question (III) in the case closer to the ab initio situation, the final mean phase error, respectively, for the three structures is 3, 26 and 28°. The combination of (a) and (b) in the upgraded algorithm has been proved crucial especially for the results concerning the larger structures. [source]

Upgrading the twin variables algorithm for large structures

K. Bethanis
Phase extension from lower to higher resolution by using an upgraded TWIN variables algorithm [Hountas & Tsoucaris (1995). Acta Cryst. A51, 754,763] in protein molecules with close to 1000 non-H atoms is presented. Three points of this procedure are of particular interest. (i) The use of a set of auxiliary variables providing a satisfactory fit for many kinds of constraints: the new algorithm works efficiently despite the extreme `dilution' of very limited initial phase information into a much larger set of auxiliary variables. (ii) The extension of this auxiliary variables set beyond the resolution of the observed data, which enhances the phase extension in a so-called `super-resolution' sphere. (iii) The use of the crystallographic symmetry as a new figure of merit and as a reliable test for the correctness of the phase-extension process allows an efficient screening. [source]

Change in electronic structure in a six-coordinate copper(II) complex accompanied by an anion order/disorder transition

Colin A. Kilner
A variable-temperature crystallographic study of [Cu(LOH)2][ClO4]2·2(CH3)2CO [LOH = 2,6-bis(hydroxyiminomethyl)pyridine] between 30 and 300,K is presented. The complex exhibits an unusual electronic structure at room temperature with a {}1 ground state, corresponding to an axially compressed ligand coordination geometry about the copper ion. This reflects a suppression of the pseudo-Jahn,Teller distortion that is normally shown by copper(II) compounds with this ligand geometry [Halcrow et al. (2004). New J. Chem.28, 228,233]. On cooling the compound undergoes an abrupt structural change at 157,±,3,K, that does not involve a change in the space group (P), but causes significant changes to c and the unit-cell angles. This reflects a conformational rearrangement of the complex dication, towards a more typical pseudo-Jahn,Teller elongated coordination geometry. This occurs concurrently with a crystallographic ordering of one of the two perchlorate anions, and a significant displacement of the two lattice acetone molecules. The transformation involves displacements of up to 0.5,Å in the non-H atoms of the structure at 30,K, compared with their positions at 300,K. The change in coordination geometry of the complex around 157,K is reflected in a small reduction in its magnetic moment near that temperature. [source]

(E)-3-(4-Methylphenyl)-2-(2-thienyl)acrylonitrile has Z, = 0.75 in the space group C2/m: fourfold disordered molecules lie in channels enclosed by fully ordered molecules

Debora Cobo
The title compound, C14H11NS, crystallizes with Z, = 0.75 in the space group C2/m. Two independent molecules are present, one of which lies with all the non-H atoms on a mirror plane, while the other is fourfold disordered across a site of 2/m symmetry. The ordered molecules are stacked such that they enclose continuous channels running along twofold rotation axes, and the disordered molecules are positioned within these channels. [source]

(E)-Methyl 2-[(2-fluorophenyl)aminomethylene]-3-oxobutanoate: X-ray and density functional theory (DFT) study

Vratislav Langer
The title compound, C12H12FNO3, a potential precursor for fluoroquinoline synthesis, is essentially planar, with the most outlying atoms displaced from the best-plane fit through all non-H atoms by 0.163,(2) and 0.118,(2),Å. Molecules are arranged in layers oriented parallel to the (011) plane. The arrangement of the molecules in the structure is controlled mainly by electrostatic interactions, as the dipole moment of the molecule is 5.2,D. In addition, the molecules are linked by a weak C,H...O hydrogen bond which gives rise to chains with the base vector [1,1,1]. Electron transfer within the molecule is analysed using natural bond orbital (NBO) analysis. Deviations from the ideal molecular geometry are explained by the concept of non-equivalent hybrid orbitals. [source]

N - tert -Butyl- N,-(5,7-di­methyl-1,8-naphthyridin-2-yl)­urea

Ulrich Lüning
The title compound, C15H20N4O, has been synthesized as an AADD recognition unit for quadruple hydrogen bonds. All non-H atoms of the mol­ecule apart from two methyl groups of the tert -butyl group lie in a common plane. An intramolecular hydrogen bond is formed connecting two N atoms. In the solid state, the title compound crystallizes as a centrosymmetric dimer connected by N,H,O=C interactions with an N,O distance of 2.824,(2),Å. [source]

On the use of logarithmic scales for analysis of diffraction data

Alexandre Urzhumtsev
Predictions of the possible model parameterization and of the values of model characteristics such as R factors are important for macromolecular refinement and validation protocols. One of the key parameters defining these and other values is the resolution of the experimentally measured diffraction data. The higher the resolution, the larger the number of diffraction data Nref, the larger its ratio to the number Nat of non-H atoms, the more parameters per atom can be used for modelling and the more precise and detailed a model can be obtained. The ratio Nref/Nat was calculated for models deposited in the Protein Data Bank as a function of the resolution at which the structures were reported. The most frequent values for this distribution depend essentially linearly on resolution when the latter is expressed on a uniform logarithmic scale. This defines simple analytic formulae for the typical Matthews coefficient and for the typically allowed number of parameters per atom for crystals diffracting to a given resolution. This simple dependence makes it possible in many cases to estimate the expected resolution of the experimental data for a crystal with a given Matthews coefficient. When expressed using the same logarithmic scale, the most frequent values for R and Rfree factors and for their difference are also essentially linear across a large resolution range. The minimal R -factor values are practically constant at resolutions better than 3,Å, below which they begin to grow sharply. This simple dependence on the resolution allows the prediction of expected R -factor values for unknown structures and may be used to guide model refinement and validation. [source]