Rapid neutron-diffraction data collection for hydrogen-bonding studies: application of the Laue diffractometer (LADI) to the case study zinc (tris)thiourea sulfate

2001 ◽  
Vol 57 (4) ◽  
pp. 429-434 ◽  
Author(s):  
Jacqueline M. Cole ◽  
Garry J. McIntyre ◽  
Mogens S. Lehmann ◽  
Dean A. A. Myles ◽  
Clive Wilkinson ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Data Collection ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Neutron Diffraction Data

Design of a novel Peltier-based cooling device and its use in neutron diffraction data collection of perdeuterated yeast pyrophosphatase

2010 ◽  
Vol 43 (5) ◽  
pp. 1113-1120 ◽  
Author(s):  
Esko Oksanen ◽  
François Dauvergne ◽  
Adrian Goldman ◽  
Monika Budayova-Spano
Keyword(s):  
Data Collection ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Catalytic Mechanism ◽  
Inorganic Pyrophosphatase ◽  
Neutron Diffraction Data ◽  
Cooling Device ◽  
Data Set ◽  
X Ray ◽  
X Ray Crystallography

H atoms play a central role in enzymatic mechanisms, but H-atom positions cannot generally be determined by X-ray crystallography. Neutron crystallography, on the other hand, can be used to determine H-atom positions but it is experimentally very challenging. Yeast inorganic pyrophosphatase (PPase) is an essential enzyme that has been studied extensively by X-ray crystallography, yet the details of the catalytic mechanism remain incompletely understood. The temperature instability of PPase crystals has in the past prevented the collection of a neutron diffraction data set. This paper reports how the crystal growth has been optimized in temperature-controlled conditions. To stabilize the crystals during neutron data collection a Peltier cooling device that minimizes the temperature gradient along the capillary has been developed. This device allowed the collection of a full neutron diffraction data set.

Real-time swelling-series method improves the accuracy of lamellar neutron-diffraction data

2000 ◽  
Vol 56 (1) ◽  
pp. 48-54 ◽  
Author(s):  
Malcolm J. M. Darkes ◽  
Jeremy P. Bradshaw
Keyword(s):  
Quantitative Analysis ◽  
Relative Humidity ◽  
Data Collection ◽  
Neutron Diffraction ◽  
Real Time ◽  
Diffraction Data ◽  
Series Method ◽  
Neutron Diffraction Data ◽  
Smooth Curves ◽  
Structure Factors

Neutron-diffraction data were collected from stacked bilayers of 1,2-dioleoyl-sn-glycero-phosphocholine under conditions of increasing relative humidity at both 0 and 8.06% 2H2O. Over the period of data collection, the d-repeat of both swelling-series samples increased. Each family of structure factors, representing each of the five orders of diffraction, are shown to lie on smooth curves, allowing structure factors of intermediate d-repeat to be determined. In the case of the 8.06% 2H2O data, but not the 0% 2H2O data, all observed structure factors lie on a single continuous transform. 8.06% 2H2O has a net neutron-scattering density of zero; its use in neutron-diffraction experiments presents a novel application of the so-called `minus fluid' approach, without mathematical manipulation. The data are used to demonstrate the increased accuracy inherent in this real-time swelling-series approach. A quantitative analysis of errors caused by differences in d-repeat in difference subtractions is presented.

scholarly journals Glycyl-L-alanine: a multi-temperature neutron study

2014 ◽  
Vol 70 (10) ◽  
pp. 949-952 ◽  
Author(s):  
Silvia C. Capelli ◽  
Hans-Beat Bürgi ◽  
Sax A. Mason ◽  
Dylan Jayatilaka
Keyword(s):  
Hydrogen Bonding ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Neutron Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hydrogen Bonding Interactions ◽  
Anisotropic Displacement Parameters

Neutron diffraction data have been collected at 12, 50, 150 and 295 K for the dipeptide glycyl-L-alanine, C5H10N2O3, in order to obtain accurate positional and anisotropic displacement parameters for the H atoms. The values of these parameters serve as a benchmark for assessing the equivalent parameters obtained from a so-called Hirshfeld-atom refinement of X-ray diffraction data described elsewhere [Capelliet al.(2014).IUCrJ,1, 361–379]. The flexibility of the glycyl-L-alanine molecule in the solid and the hydrogen-bonding interactions as a function of temperature are also considered.

Migration of the proton in the strong O—H...O hydrogen bond in urea–phosphoric acid (1/1)

2001 ◽  
Vol 57 (3) ◽  
pp. 435-439 ◽  
Author(s):  
Chick C. Wilson
Keyword(s):  
Hydrogen Bond ◽  
Data Collection ◽  
Neutron Diffraction ◽  
Phosphoric Acid ◽  
Diffraction Data ◽  
Accurate Determination ◽  
Neutron Diffraction Data ◽  
Crystal Data ◽  
Collection Method

The structure of urea–phosphoric acid is reported at a large number of temperatures in the range 150–335 K from neutron diffraction data collected using a novel multiple single-crystal data collection method. The work focuses on the behaviour of the H atom involved in the short strong O—H...O hydrogen bond in this material. The position of this atom is shown to vary significantly, by around 0.035  Å, as a function of temperature, becoming effectively centred at the highest temperatures studied. This result, only accessible due to the accurate determination of H-atom parameters by neutron diffraction, has implications for the potential governing the hydrogen bond.

scholarly journals Cryo-neutron crystallographic data collection and preliminary refinement of left-handed Z-DNA d(CGCGCG)

2018 ◽  
Vol 74 (10) ◽  
pp. 603-609 ◽  
Author(s):  
Joel M. Harp ◽  
Leighton Coates ◽  
Brendan Sullivan ◽  
Martin Egli
Keyword(s):  
Low Temperature ◽  
Data Collection ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Water Molecules ◽  
X Rays ◽  
Neutron Diffraction Data ◽  
Oak Ridge ◽  
Left Handed ◽  
Z Dna

Crystals of left-handed Z-DNA [d(CGCGCG)]2 diffract X-rays to beyond 1 Å resolution, feature a small unit cell (∼18 × 31 × 44 Å) and are well hydrated, with around 90 water molecules surrounding the duplex in the asymmetric unit. The duplex shows regular hydration patterns in the narrow minor groove, on the convex surface and around sugar–phosphate backbones. Therefore, Z-DNA offers an ideal case to test the benefits of low-temperature neutron diffraction data collection to potentially determine the donor–acceptor patterns of first- and second-shell water molecules. Nucleic acid fragments pose challenges for neutron crystallography because water molecules are located on the surface rather than inside sequestered spaces such as protein active sites or channels. Water molecules can be expected to display dynamic behavior, particularly in cases where water is not part of an inner shell and directly coordinated to DNA atoms. Thus, nuclear density maps based on room-temperature diffraction data with a resolution of 1.6 Å did not allow an unequivocal determination of the orientations of water molecules. Here, cryo-neutron diffraction data collection for a Z-DNA crystal on the Macromolecular Neutron Diffractometer at the Spallation Neutron Source at Oak Ridge National Laboratory and the outcome of an initial refinement of the structure are reported. A total of 12 diffraction images were recorded with an exposure time of 3.5 h per image, whereby the crystal was static for each diffraction image with a 10° φ rotation between images. Initial refinements using these neutron data indicated the positions and orientations of 30 water molecules within the first hydration shell of the DNA molecule. This experiment constitutes a state-of-the-art approach and is the first attempt to our knowledge to determine the low-temperature neutron structure of a DNA crystal.

A neutron-diffraction study of potassium bromide

1973 ◽  
Vol 137 (4) ◽  
Author(s):  
G. E. Bacon ◽  
D. H. Titterton ◽  
C. R. Walker
Keyword(s):  
Neutron Diffraction ◽  
Diffraction Data ◽  
Diffuse Scattering ◽  
Scattering Amplitude ◽  
Coherent Scattering ◽  
Neutron Diffraction Study ◽  
Potassium Bromide ◽  
Neutron Diffraction Data ◽  
Thermal Diffuse Scattering ◽  
Thermal Diffuse

AbstractNeutron-diffraction data have been collected from a KBr single crystal. 380 reflections were measured, reducing to 23 when averaged over equivalents. Data were corrected for extinction and thermal diffuse scattering and refinement yielded a neutron coherent scattering amplitude

Extracting fluid structures from neutron diffraction data

1995 ◽  
Vol 236 (1-2) ◽  
pp. 1-7 ◽  
Author(s):  
Haluk Resat ◽  
Enci Zhong ◽  
Harold L. Friedman
Keyword(s):  
Neutron Diffraction ◽  
Diffraction Data ◽  
Neutron Diffraction Data
Sign in / Sign up

Export Citation Format

Share Document