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PubMed2000

Quantitative analysis of hydrogen bonding and atomic thermal motion in the organic non-linear optical material DCNP using X-ray and neutron diffraction

A single-crystal neutron diffraction study of the organic non-linear optical material 3-(1,1-dicyanoethenyl)-1-phenyl-4, 5-dihydro-1H-pyrazole (hereafter DCNP), space group Cc, is presented. The study was conducted in order to relate the structural characteristics of the compound to its physical properties. DCNP exhibits a very large second harmonic generation (SHG) output, an extremely large linear electro-optical effect and photoconductive and pyroelectric properties. The nature of the hydrogen-bonding revealed by the study, in part, accounts for the first two of these phenomena. The neutron study also shows that some rather atypical atomic thermal motion is present in part of the molecule. With the aid of a variable-temperature single-crystal X-ray diffraction study, in conjunction with the neutron study, this thermal motion is attributed to libration and is fully characterized. As a result, suitable corrections to the bond geometry and the anisotropic displacement parameters of DCNP are made. The libration is also shown to enhance the SHG effect. The cell parameters from the variable-temperature X-ray study are also used in order to evaluate the thermal expansivity coefficients of DCNP.

Journal Article↗
PubMed1993

The in vivo glycation of diabetic tendon collagen studied by neutron diffraction.

Glycation (non-enzymatic glycosylation) sites in the axial unit cell of diabetic tendon collagen were investigated by neutron diffraction. Samples of diabetic and control tendon were reacted with sodium borodeuteride and sodium cyanoborodeuteride. This facilitated deuteration at aldimine, aldol or ketoimine groups in the molecule. These are natural collagen cross-links and sites where non-enzymatic glycation had occurred. The introduction of a deuteron at specific locations allowed the diabetic glycation collagen to be treated as multiple isomorphous derivatives for neutron fibre diffraction. Neutron diffraction was conducted at the Institut Laue Langevin, Grenoble. Standard crystallographic refinement techniques (modified for axial projections) were used to determine the structure of the control (non-diabetic) and diabetic samples. The results are shown as difference maps, these indicate that glycation takes place at different rates within the collagen axial unit cell. The position of glycation correlates well with the position of hydroxylysine residues. The reactions of periodate with enzymatically attached sugars, proteoglycan, natural cross-links and glycation products lead to complications in map interpretation.

Animals↗
PubMed1988

Determination of the absolute configuration of (-)-(2R)-succinic-2-d acid by neutron diffraction study: unambiguous proof of the absolute stereochemistry of the NAD+/NADH interconversion.

The absolute configuration of the CHD group (D = deuterium) in (-)-(2R)-succinic-2-d acid, as prepared from (-)-(2S,3R)-malic-3-d acid, has been shown unambiguously to be R by the technique of single-crystal neutron diffraction. The optically active cation (+)-phenylethylammonium was used as the chiral reference. The structure of [C6H5CH3CHNH3]+[HOOCCH2CHDCOO]- has been studied with x-ray diffraction at room temperature and neutron diffraction at 100 K. Crystal data from the neutron diffraction analysis of the phenylethylammonium salt of the title compound at 100 K: space group P21; a = 8.407(2) A, b = 8.300(4) A, c = 8.614(2) A, beta = 91.20(3) degrees; unit cell volume = 600.9(3) A3, zeta = 2 (numbers in parentheses are the estimated standard deviations). Final agreement factors are R(F2) = 0.0355 and R(wF2) = 0.0457 for 1690 independent neutron reflections and 297 parameters varied. The result confirms the stereochemistry of the malate/succinate transformation, as well as the NAD+/NADH interconversion, and demonstrates the usefulness of the single-crystal neutron diffraction method for determining the absolute configuration of molecules having a chiral monodeuteriomethylene group.

Chemical Phenomena↗
PubMed1969

Neutron diffraction of cell membranes (myelin).

Small-angle neutron diffraction (wavelength 4.05 angstroms) of human and rabbit sciatic nerve has been carried out by means of the Brookhaven high flux beam reactor with an automated slit camera. Most of the free water of the nerves was substituted in order to minimize incoherent scatter of hydrogen atoms. The differences in amplitude and phase shifts between neutrons and x-rays resulted in a neutron diffraction pattern that was completely different from the x-ray pattern. The neutron pattern consisted of a single peak of about 89-angstrom spacing in the region examined (up to 6-angstrom spacing). The strong third, fourth, and fifth order reflections (about 60, 45, and 36 angstroms) seen in the x-ray pattern were suppressed. The neutron data indicated a strong scattering from one portion of the membrane.

Animals↗
PubMed1982

Biochemical profiles of membranes from x-ray and neutron diffraction.

X-ray and neutron diffraction methods provide some information about the distribution of mass in biological membranes and lipid-water systems. Scattering density profiles obtained from these systems, however, usually are not directly interpretable in terms of the relative amounts of chemical constituents (e.g., lipid, protein, and water) as a function of position in the membrane. We demonstrate here that the combined use of x-ray and neutron-scattering profiles, together with information on the total amounts of each of the major membrane components, are sufficient to calculate unambiguously the volume fractions of these components at well-defined regions of the lamellar unit. Three cases are considered: a calculated model membrane pair, dipalmitoylphosphatidylcholine-water multilayers, and rabbit sciatic nerve myelin. For the model system, we discuss the limitations imposed by finite resolution in the diffraction patterns. For the lipid-water multilayers, we calculate water volume fractions in the hydrocarbon tail, lipid headgroup, and interlamellar regions; estimates of these values by various methods are in good agreement with our results. For the nerve myelin, we predict new results for the distribution of protein through the membrane.

Animals↗
PubMed1979

Neutron diffraction studies of lumbar vertebrae.

Neutron diffraction measurements of the orientation of the apatite crystals show a significant preference of their c-axes for the vertical direction. This preference increases from bottom to top of each vertebral body and is substantially greater for the second than for the fifth lumbar vertebrae. This is in line with the predominantly vertical forces which the former withstands.

Apatites↗
PubMed1991

Effects of physiologically relevant pressures of helium on the structure of cholesterol-containing lipid bilayers. A neutron diffraction study.

We have used neutron diffraction to study the effects of helium gas (1-210 atm) on the structure of a lipid bilayer model of neuronal plasma membranes. We have recorded diffraction patterns from hydrated multilayers of dimyristoyl lecithin and 40% (molar) cholesterol to a resolution of approximately 6.5 A and have calculated scattering amplitude density distributions as a function of pressure. We find that there are no significant changes in the scattering density profiles at 95% confidence over the range of pressures investigated, suggesting that the physiological effects of high helium pressure are unlikely to be a consequence of changes in the structures of the lipid bilayer portions of membranes.

Biophysical Phenomena↗
PubMed2003

Field-induced ferromagnetic metallic state of bilayer manganite (La0.4Pr0.6)1.2Sr1.8Mn2O7: a polarized neutron diffraction study.

Unpolarized and polarized neutron diffraction measurements have been carried out on the bilayer manganite (La0.4Pr0.6)1.2Sr1.8Mn2O7 which undergoes simultaneous semiconductor-metal paraferromagnetic transitions under magnetic field. Maximum entropy magnetization density reconstruction and multipole refinement on flipping ratios evidence the existence of two distinct field-induced states. The field-induced ferromagnetic state where the field is parallel to the c axis is characterized by the presence of magnetic moment on the Sr site of 0.48(2)mu(B), due to the Pr substitution. It also shows a high population of the d3(z(2)-r(2)) orbitals of Mn3+. For the field-induced state where the field is parallel to the a or b axes no magnetization density was found at the Sr site and the dx(2)(-y(2)) orbital is slightly more populated than the d3(z(2)-r(2)) one.

Journal Article↗
PubMed1988

Conformation of the coat protein of filamentous bacteriophage Pf1 determined by neutron diffraction from magnetically oriented gels of specifically deuterated virions.

The structure of filamentous bacteriophage Pf1 has been studied using neutron diffraction from magnetically oriented gels of native and valine-deuterated phage. Neutron diffraction intensities were measured to approximately 8 A resolution along the equator and first six layer-lines, and differences due to the deuterated valine residues were apparent. Analysis of equatorial data indicate that one valine residue is located at a radius of about 13 A, three are in the hydrophobic center of the protein coat at an average of about 22 A radius, and one is near the outer surface of the virion at about 28 A radius. Analysis of the three-dimensional data was initiated using the rod model for the alpha-helices of the coat protein derived from earlier X-ray diffraction studies. This model was refined against the neutron diffraction intensities from native phage to obtain a phase set that was used to calculate a difference map between the valine-deuterated and native phage. The difference map exhibits peaks that correspond to the positions of the five valine residues in the coat protein. From the amino acid sequence and the alpha-helical conformation of the coat protein, the five valine residues can be unambiguously assigned to the difference peaks. This assignment indicates that the two alpha-helices of the coat protein are parallel to one another, connected by a short stretch of non-helical peptide. The valine positions also indicate that the helical surface lattice of the phage particle is right-handed.

Amino Acid Sequence↗
PubMed1992

Solvent structure in crystals of trypsin determined by X-ray and neutron diffraction.

The solvent structure in orthorhombic crystals of bovine trypsin has been independently determined by X-ray diffraction to 1.35 A resolution and by neutron diffraction to 2.1 A resolution. A consensus model of the water molecule positions was obtained using oxygen positions identified in the electron density map determined by X-ray diffraction, which were verified by comparison to D2O-H2O difference neutron scattering density. Six of 184 water molecules in the X-ray structure, all with B-factors greater than 50 A2, were found to be spurious after comparison with neutron results. Roughly two-thirds of the water of hydration expected from thermodynamic data for proteins was localized by neutron diffraction; approximately one-half of the water of hydration was located by X-ray diffraction. Polar regions of the protein are well hydrated, and significant D2O-H2O difference density is seen for a small number of water molecules in a second shell of hydration. Hydrogen bond lengths and angles calculated from unconstrained refinement of water positions are distributed about values typically seen in small molecule structures. Solvent models found in seven other bovine trypsin and trypsinogen and rat trypsin structures determined by X-ray diffraction were compared. Internal water molecules are well conserved in all trypsin structures including anionic rat trypsin, which is 65% homologous to bovine trypsin. Of the 22 conserved waters in trypsin, 19 were also found in trypsinogen, suggesting that they are located in regions of the apoprotein that are structurally conserved in the transition to the mature protein. Seven waters were displaced upon activation of trypsinogen. Water structure at crystal contacts is not generally conserved in different crystal forms. Three groups of integral structural water molecules are highly conserved in all solvent structures, including a spline of water molecules inserted between two beta-strands, which may resemble an intermediate in the formation of beta sheets during the folding of a protein.

Deuterium↗
PubMed1999

X-ray and neutron diffraction study of benzoylacetone in the temperature range 8-300 K: comparison with other cis-enol molecules.

The crystal structure of benzoylacetone (1-phenyl-1,3-butanedione, C(10)H(10)O(2); P2(1)/c, Z = 4) has been determined at 300, 160 (both Mo Kalpha X-ray diffraction, XRD), 20 (lambda = 1.012 Å neutron diffraction, ND) and 8 K (Ag Kalpha XRD), to which should be added earlier structure determinations at 300 (Mo Kalpha XRD and ND, lambda = 0.983 Å) and 143 K (Mo Kalpha XRD). Cell dimensions have been measured over the temperature range 8-300 K; a first- or second-order phase change does not occur within this range. The atomic displacement parameters have been analyzed using the thermal motion analysis program THMA11. The most marked change in the molecular structure is in the disposition of the methyl group, which has a librational amplitude of approximately 20 degrees at 20 K and is rotationally disordered at 300 K. The lengths of the two C-O bonds in the cis-enol ring do not differ significantly, nor do those of the two C-C bonds, nor do these lengths change between 8 and 300 K. An ND difference synthesis (20 K) shows a single enol hydrogen trough (rather than two half H atoms), approximately centered between the O atoms; analogous results were obtained by XRD (8 K). It is inferred that the enol hydrogen is in a broad, flat-bottomed single-minimum potential well between the O atoms, with a libration amplitude of approximately 0.30 Å at 8 K. These results suggest that at 8 K the cis-enol ring in benzoylacetone has quasi-aromatic character, in agreement with the results of high-level ab initio calculations made for benzoylacetone [Schiøtt et al. (1998). J. Am. Chem. Soc. 120, 12117-12124]. Application [in a related paper by Madsen et al. (1998). J. Am. Chem. Soc. 120, 10040-10045] of multipolar analysis and topological methods to the charge density obtained from the combined lowest temperature X-ray and neutron data provides evidence for an intramolecular hydrogen bond with partly electrostatic and partly covalent character, and large p-delocalization in the cis-enol ring. This is in good agreement with what is expected from the observed bond lengths. Analysis of the total available (through the Cambridge Structural Database, CSD) population of cis-enol ring geometries confirms earlier reports of correlation between the degree of bond localization in the pairs of C-C and C-O bonds, but does not show the dependence of bond localization on d(O.O) that was reported earlier for a more restricted sample. It is suggested that the only reliable method of determining whether the enol hydrogen is found in a single or double potential well is by low-temperature X-ray or (preferably) neutron diffraction.

Journal Article↗
PubMed1987

The transducin cascade is involved in the light-induced structural changes observed by neutron diffraction on retinal rod outer segments.

Time-resolved neutron diffraction on retinal rod outer segments are performed to reinvestigate the origin of the light-induced structural change observed by Saibil et al. (Saibil, H., M. Chabre, and D. L. Worcester, 1976, Nature (Lond.), 262:266-270). Photoactivating rhodopsin triggers in rods a cascade of GTP-dependent and transducin-mediated reactions controlling cyclic-GMP hydrolysis. Infrared light-scattering studies (Kühn, H., N. Bennett, M. Michel-Villaz, and M. Chabre, 1981, Proc. Natl. Acad. Sci. USA, 78:6873-6877; Vuong, T. M., M. Chabre, and L. Stryer, 1984, Nature (Lond.), 311:659-661) demonstrated the existence of structural changes that correspond to this cascade rather than to rhodopsin photoactivation. We thus look for neutron diffraction changes of similar origins. With 1-min time resolution, intensity changes are observed mainly for orders 2 and 4. The illumination and GTP dependence of these changes indicates an involvement of transducin. Without GTP, they are linear with the amount of photoexcited rhodopsin, saturate at 10% photolysis, and thus correlate well with the light-scattering "binding signal." With GTP, light sensitivity is higher and saturation occurs below 0.5% photolysis, as for the "dissociation signal" of light scattering. In both cases, lattice compressions of 0.2-0.3% are observed. With 4-s time resolution the intensity change with GTP present precedes the lattice compression. The fast intensity change is probably due to the displacement of transducin alpha-subunits away from the disc membrane and the slower lattice shrinkage to an osmotic readjustment of the rod.

Animals↗
PubMed1985

The separate profile structures of the functional calcium pump protein and the phospholipid bilayer within isolated sarcoplasmic reticulum membranes determined by X-ray and neutron diffraction.

The detailed profile structure of the isolated sarcoplasmic reticulum membrane was studied utilizing a combination of X-ray and neutron diffraction. The water and lipid profile structures within the sarcoplasmic reticulum membrane were determined at 28 A resolution directly by neutron diffraction and selective deuteration of the water and lipid components. The previously determined electron density profile structure of the sarcoplasmic reticulum membrane at 12 A resolution was subjected to model refinement analysis constrained by the neutron diffraction results, thereby providing unique higher resolution calculated lipid and protein profile structures. It was found that the lipid bilayer profile structure of the isolated sarcoplasmic reticulum membrane is asymmetric, primarily the result of more lipid residing in the inner versus the outer monolayer of the sarcoplasmic reticulum lipid bilayer. The asymmetry in the lipid composition was necessarily coincident with a complimentary asymmetry in the protein mass distribution between the two monolayers in order to preserve the overall cross-sectional area of lipid and protein throughout the lipid bilayer region of the sarcoplasmic reticulum membrane profile structure. Approximately 50% of the mass of the total protein was found to be localized externally to the sarcoplasmic reticulum membrane lipid bilayer protruding from the outer lipid monolayer into the extravesicular medium. The structural features of the protein protrusion appear to be rather variable depending upon the environment of the sarcoplasmic reticulum membrane. This highly asymmetric structural organization of the sarcoplasmic reticulum membrane profile is consistent with its primary function of unidirectional calcium transport.

Animals↗
PubMed1996

The chemical reactivity and structure of collagen studied by neutron diffraction.

The chemical reactivity of collagen can be studied using neutron diffraction (a non-destructive technique), for certain reaction types. Collagen contains a number of lysine and hydroxylysine side chains that can react with aldehydes and ketones, or these side chains can themselves be converted to aldehydes by lysyl oxidase. The reactivity of these groups not only has an important role in the maintenance of mechanical strength in collagen fibrils, but can also manifest pathologically in the cases of aging, diabetes (reactivity with a variety of sugars) and alcoholism (reactivity with acetaldehyde). The reactivity of reducing groups with collagen can be studied by neutron diffraction, since the crosslink formed in the adduction process is initially of a Schiff base or keto-imine nature. The nature of this crosslink allows it to be deuterated, and the position of this relatively heavy scattering atom can be used in a process of phase determination by multiple isomorphous replacement. This process was used to study the following: the position of natural crosslinks in collagen; the position of adducts in tendon from diabetic rats in vivo and the in vitro position of acetaldehyde adducts in tendon.

Acetaldehyde↗
PubMed2003

Determination of the number of water molecules in the proton pathway of bacteriorhodopsin using neutron diffraction data.

It has been shown that water molecules participate in the proton pathway of bacteriorhodopsin. Large efforts have been made to determine with various biophysical methods the number of water molecules involved. Neutron diffraction H2O/D2O exchange experiments have been often used to reveal the position of water even with low-resolution diffraction data. With this technique, care must be taken with the limitations of the difference Fourier method which are commonly applied to analyze the data. In this paper we compare the results of the difference Fourier method applied to measured diffraction data (not presented here) and models with those from alternative methods introduced here: (1) a computer model calculation procedure to determine a label's scattering length density based on a comparison of intensity differences derived from models and intensity differences from our measurements; (2) a method based on the Parseval formula. Both alternative methods have been evaluated and tested using results of neutron diffraction experiments on purple membranes (Hauss et al. 1994). Our findings indicate that the difference Fourier method applied to low-resolution diffraction data can successfully determine the position of localized water molecules but underestimates their integrated scattering length density in the presence of labels in other positions. Furthermore, we present the results of neutron diffraction experiments on purple membranes performed to determine the number of water molecules in the projected area of the Schiff base at 86%, 75% and 57% relative humidity (r.h.). We found 19 +/- 2 exchangeable protons at 75% r.h., which means at least 8-9 water molecules are indispensable for normal pump function.

Algorithms↗
PubMed2003

Membrane insertion of a lipidated ras peptide studied by FTIR, solid-state NMR, and neutron diffraction spectroscopy.

Membrane binding of a doubly lipid modified heptapeptide from the C-terminus of the human N-ras protein was studied by Fourier transform infrared, solid-state NMR, and neutron diffraction spectroscopy. The 16:0 peptide chains insert well into the 1,2-dimyristoyl-sn-glycero-3-phosphocholine phospholipid matrix. This is indicated by a common main phase transition temperature of 21.5 degrees C for both the lipid and peptide chains as revealed by FTIR measurements. Further, (2)H NMR reveals that peptide and lipid chains have approximately the same chain length in the liquid crystalline state. This is achieved by a much lower order parameter of the 16:0 peptide chains compared to the 14:0 phospholipid chains. Finally, proton/deuterium contrast variation of neutron diffraction experiments indicates that peptide chains are localized in the membrane interior analogous to the phospholipid chains. In agreement with this model of peptide chain insertion, the peptide part is localized at the lipid-water interface of the membrane. This is revealed by (1)H nuclear Overhauser enhancement spectra recorded under magic angle spinning conditions. Quantitative cross-peak analysis allows the examination of the average location of the peptide backbone and side chains with respect to the membrane. While the backbone shows the strongest cross-relaxation rates with the phospholipid glycerol, the hydrophobic side chains of the peptide insert deeper into the membrane interior. This is supported by neutron diffraction experiments that reveal a peptide distribution in the lipid-water interface of the membrane. Concurring with these experimental findings, the amide protons of the peptide show strong water exchange as seen in NMR and FTIR measurements. No indications for a hydrogen-bonded secondary structure of the peptide backbone are found. Therefore, membrane binding of the C-terminus of the N-ras protein is mainly due to lipid chain insertion but also supported by interactions between hydrophobic side chains and the lipid membrane. The peptide assumes a mobile and disordered conformation in the membrane. Since the C-terminus of the soluble part of the ras protein is also disordered, we hypothesize that our model for membrane binding of the ras peptide realistically describes the membrane binding of the lipidated C-terminus of the active ras protein.

Dimyristoylphosphatidylcholine↗
PubMed2000

X-ray and neutron diffraction studies of crystallinity in hydroxyapatite coatings.

To standardize industrial implant production and make comparisons between different experimental results, we have to be able to quantify the crystallinity of hydroxyapatite. Methods of measuring crystallinity ratio were developed for various HA samples before and after plasma spraying. The first series of methods uses X-ray diffraction. The advantage of these methods is that X-ray diffraction equipment is used widely in science and industry. In the second series, a neutron diffraction method is developed and the results recorded are similar to those obtained by the modified X-ray diffraction methods. The advantage of neutron diffraction is the ability to obtain measurements deep inside a component. It is a nondestructive method, owing to the very low absorption of neutrons in most materials.

Biocompatible Materials↗
PubMed1990

Water molecules and exchangeable hydrogen ions at the active centre of bacteriorhodopsin localized by neutron diffraction. Elements of the proton pathway?

Neutron diffraction is used to localize water molecules and/or exchangeable hydrogen ions in the purple membrane by H2O/2H2O exchange experiments at different values of relative humidity. At 100% relative humidity, differences in the hydration between protein and lipid areas are observed, accounting for an excess amount of about 100 molecules of water in the lipid domains per unit cell. A pronounced isotope effect was observed, reproducibly showing an increase in the lamellar spacing from 60 A in 2H2O to 68 A in H2O. At 15% relative humidity, the positions of exchangeable protons became visible. A dominant difference density peak corresponding to 11 +/- 2 exchangeable protons was detected in the central part of the projected structure of bacteriorhodopsin at the Schiff's base end of the chromophore. A difference density map obtained from data on purple membrane films at 15% relative humidity in 2H2O, and the same sample after complete drying in vacuum, revealed that about eight of these protons belong to four water molecules. This is direct evidence for tightly bound water molecules close to the chromophore binding site of bacteriorhodopsin, which could participate in the active steps of H+ translocation as well as in the proton pathway across this membrane protein.

Bacteriorhodopsins↗