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PubMed1980

Neutron diffraction identifies His 57 as the catalytic base in trypsin.

The mechanism of action of trypsin and other serine proteases has been widely debated, particularly with regard to the identification of the group at the active site which functions as the chemical base during the catalytic process. Attempts to resolve this question by a number of indirect techniques, including NMR, isotope exchange, difference IR and quantum mechanical calculations, have resulted in different identifications of this group. Neutron diffraction, because of its ability to locate hydrogen atoms experimentally, offers the most direct way of resolving this issue. Results are presented here from a 2.2-A neutron data set for bovine trypsin covalently inhibited by a transition-state analogue, the monoisopropylphosphoryl (MIP) group. His 57 is clearly identified as the base in the catalytic process.

Amino Acid Sequence↗
PubMed2002

Electron distribution and molecular motion in crystalline benzene: an accurate experimental study combining CCD X-ray data on C6H6 with multitemperature neutron-diffraction results on C6D6.

The electronic properties of the benzene molecule, for example its quadrupole moment and the electric field gradients (EFG's) at the H nuclei, are of fundamental importance in theoretical and experimental chemistry. With this in mind, single-crystal X-ray diffraction data on C(6)H(6) were collected with a charge-coupled device detector at T approximately 110 K. As accurate modelling of the thermal motion in the crystal was regarded as vital, especially for the hydrogen atoms, anisotropic-displacement parameters (ADP's) for the C and H atoms in C(6)H(6) were derived in a straightforward fashion from analysis of the temperature dependence of ADP's for the C and D atoms in C(6)D(6) at 15 K and 123 K obtained by neutron diffraction. Agreement between C-atom ADP's derived from thermal-motion analysis of neutron data and those obtained from multipole refinement by using the X-ray data is extraordinarily good; this gives confidence in the modelling of vibrational motion for the H atoms. The molecular quadrupole moment derived from the total charge density of the molecule in the crystal is (-29.7+/-2.4)x10(-40) C m(2), in excellent agreement with measurements made in the gas phase and in solution. The average deuterium nuclear quadrupole coupling constant (DQCC) derived from EFG tensors at H atoms is 182+/-17 kHz, also in excellent agreement with independent measurements. The strategy employed in this work may be of more general applicability for future accurate electron density studies.

Benzene↗
PubMed2004

Modeling the structure of amorphous MoS3: a neutron diffraction and reverse Monte Carlo study.

A model for the structure of amorphous molybdenum trisulfide, a-MoS3, has been created using reverse Monte Carlo methods. This model, which consists of chains of MoS6 units sharing three sulfurs with each of its two neighbors and forming alternate long, nonbonded, and short, bonded, Mo-Mo separations, is a good fit to the neutron diffraction data and is chemically and physically realistic. The paper identifies the limitations of previous models based on Mo3 triangular clusters in accounting for the available experimental data.

Journal Article↗
PubMed2001

Lu2SiO5 by single-crystal X-ray and neutron diffraction.

The structure of dilutetium silicon pentaoxide, Lu2SiO5, has isolated ionic SiO4 tetrahedral units and non-Si-bonded O atoms in distorted OLu4 tetrahedra. The OLu4 tetrahedra form edge-sharing infinite chains and double O2Lu6 tetrahedra along the c axis. The edge-sharing chains are connected to the O2Lu6 double tetrahedra by isolated SiO4 units. The structure has been determined by neutron diffraction.

Crystallography, X-Ray↗
PubMed1994

Light-induced isomerization causes an increase in the chromophore tilt in the M intermediate of bacteriorhodopsin: a neutron diffraction study.

Bacteriorhodopsin (BR) was regenerated with two selectively deuterated retinals, one with 11 deuterons in the beta-ionone ring (D11) and the other with 5 deuterons (D5) at the end of the polyene chain closest to the Schiff base at carbon atoms C-14, C-15, and C-20. Both label positions (centers of deuteration) were obtained from difference Fourier maps of projections onto the plane of the membrane by neutron diffraction at 90 K, both in the light-adapted ground-state BR568 and in the photocycle intermediate M412. To retard the decay of M412, purple membrane films were soaked in 0.1 M or 1 M guanidine hydrochloride at pH 9.6. M412 was produced by illuminating oriented membrane films at physiological temperature (278 K), followed by rapid cooling to 90 K in the absence of light. The results show that in the projected structure the ring position is unaltered during the transition from BR568 to M412, whereas the position of the D5 label shifts by 1.4 +/- 0.9 A toward the ring. The shortened interlabel distance in the projected structure for the M412 state implies that as a result of the all-trans/13-cis isomerization, the C-5 to C-13 part of the polyene chain tilts out of the plane of the membrane toward the cytoplasm by about 11 degrees +/- 6 degrees. Pairwise comparison of data sets with the same retinal for the two photocycle states M412 and BR568 leads to four difference-density maps for the protein, which are in agreement with previous work. They show changes in the protein density near helices G and F.

Bacteriorhodopsins↗
PubMed1996

Neutron diffraction studies of amphipathic helices in phospholipid bilayers.

The structural feature which is thought to facilitate the interaction of many peptides with phospholipid bilayers is the ability to fold into an amphipathic helix. In most cases the exact location and orientation of this helix with respect to the membrane is not known, and may vary with factors such as pH and phospholipid content of the bilayer. The growing interest in this area is stimulated by indications that similar interactions can contribute to the binding of certain hormones to their cell-surface receptors. We have been using the techniques of neutron diffraction from stacked phospholipid bilayers in an attempt to investigate this phenomenon with a number of membrane-active peptides. Here we report some of our findings with three of these: the bee venom melittin; the hormone calcitonin; and a synthetic peptide representing the ion channel fragment of influenza A M2 protein.

Amino Acid Sequence↗
PubMed2006

Neutron diffraction studies of U4O9: comparison with EXAFS results.

Conradson et al. have analyzed X-ray absorption fine-structure spectra of the UO2-U4O9 system and concluded that oxygen atoms are incorporated in U4O9 as oxo groups with U-O distances in the range 1.72-1.76 A. They also found that the uranium sublattice consists of an ordered portion and an additional 'spectroscopically silent' glassy portion. We have carried out studies of powdered U4O9 by neutron diffraction which contradict these conclusions from EXAFS measurements. Our analysis shows that there are no U-O bonds shorter than 2.2 A and that U4O9 is crystallographically ordered with no evidence of a glassy structure.

Journal Article↗
PubMed2006

Competing magnetic interactions in Na10Co4O10, studied by neutron diffraction.

Na(10)Co(4)O(10) was investigated by neutron powder diffraction at 230, 70, and 4 K. The crystal structure, determined previously by X-ray diffraction on single crystals, was confirmed. Na(10)Co(4)O(10) orders magnetically below 37 K. All observed magnetic reflections could be indexed by integers (hkl) with respect to the chemical unit cell and the magnetic propagation vector q=0. The refinement was performed in the Shubnikov space group C2/c and indicated a collinear antiferromagnetic spin structure. The determined spin arrangement is consistent with the magnetic intratetramer interactions suggested previously from the analysis of magnetic susceptibility data: the magnetic moments of the central Co(III) ions of the Co(4)O(10) tetramer lie parallel to each other and couple in an antiparallel fashion to the terminal Co(II) moments. The Rietveld analysis shows that the net moments of 0.64 mu(B) per tetramer form ferromagnetic layers parallel to the ab plane. Adjacent layers are coupled antiferromagnetically along c. The spins are aligned in the ac plane along the line connecting adjacent Co(II) and Co(III) ions of the tetramer. We have determined unusually low values for the ordered magnetic moments of 2.43(5) mu(B) and 2.11(6) mu(B) for Co(III) and Co(II), respectively. The occurrence of spontaneous magnetization below 37 K indicates a slight canting of 2.2 degrees of the antiferromagnetic structure. A representation analysis shows that a weak ferromagnetic component along b is compatible with the determined antiferromagnetic structure.

Journal Article↗
PubMed2004

Electronic interaction in an outer-sphere mixed-valence double salt: a polarized neutron diffraction study of K(3)(MnO(4))(2).

The mixed-valence double salt K(3)(MnO(4))(2) crystallizes in space group P2(1)/m with Z = 2. The manganese centers Mn1 and Mn2 constitute discrete "permanganate", [Mn(VII)O(4)](-), and "manganate", [Mn(VI)O(4)](2-), ions, respectively. There is a spin-ordering transition to an antiferromagnetic state at ca. T = 5 K. The spin-density distribution in the paramagnetic phase at T = 10 K has been determined by polarized neutron diffraction, confirming that unpaired spin is largely confined to the nominal manganate ion Mn2. Through use of both Fourier refinement and maximum entropy methods, the spin on Mn1 is estimated as 1.75 +/- 1% of one unpaired electron with an upper limit of 2.5%.

Journal Article↗
PubMed1988

Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison.

A method for the prediction of hydrogen positions in proteins is presented. The method is based on the knowledge of the heavy atom positions obtained, for instance, from X-ray crystallography. It employs an energy minimization limited to the environment of the hydrogen atoms bound to a common heavy atom or to a single water molecule. The method is not restricted to proteins and can be applied without modification to nonpolar hydrogens and to nucleic acids. The method has been applied to the neutron diffraction structures of trypsin, ribonuclease A, and bovine pancreatic trypsin inhibitor. A comparison of the constructed and the observed hydrogen positions shows few deviations except in situations in which several energetically similar conformations are possible. Analysis of the potential energy of rotation of Lys amino and Ser, Thr, Tyr hydroxyl groups reveals that the conformations of lowest intrinsic torsion energies are statistically favored in both the crystal and the constructed structures.

Hydrogen↗
PubMed1997

Molecular-Based Magnetism in Bimetallic Two-Dimensional Oxalate-Bridged Networks. An X-ray and Neutron Diffraction Study.

Bimetallic, oxalate-bridged compounds with bi- and trivalent transition metals comprise a class of layered materials which express a large variety in their molecular-based magnetic behavior. Because of this, the availability of the corresponding single-crystal structural data is essential to the successful interpretation of the experimental magnetic results. We report in this paper the crystal structure and magnetic properties of the ferromagnetic compound {[N(n-C(3)H(7))(4)][Mn(II)Cr(III)(C(2)O(4))(3)]}(n)() (1), the crystal structure of the antiferromagnetic compound {[N(n-C(4)H(9))(4)][Mn(II)Fe(III)(C(2)O(4))(3)]}(n)() (2), and the results of a neutron diffraction study of a polycrystalline sample of the ferromagnetic compound {[P(C(6)D(5))(4)][Mn(II)Cr(III)(C(2)O(4))(3)]}(n)() (3). Crystal data: 1, rhombohedral, R3c, a = 9.363(3) Å, c = 49.207(27) Å, Z = 6; 2, hexagonal, P6(3), a = 9.482(2) Å, c = 17.827(8) Å, Z = 2. The structures consist of anionic, two-dimensional, honeycomb networks formed by the oxalate-bridged metal ions, interleaved by the templating cations. Single-crystal field dependent magnetization measurements as well as elastic neutron scattering experiments on the manganese(II)-chromium(III) samples show the existence of long-range ferromagnetic ordering behavior below T(c) = 6 K. The magnetic structure corresponds to an alignment of the spins perpendicular to the network layers. In contrast, the manganese(II)-iron(III) compound expresses a two-dimensional antiferromagnetic ordering.

Journal Article↗
PubMed2005

Single-crystal neutron-diffraction study of 3.4% Zn-doped (ND4)2[Cu(D2O)6](SO4)2 at 20 K.

Doping the perdeuterated ammonium copper Tutton salt (ND4)2[Cu(D2O)6](SO4)2 [perdeuterated diammonium hexaaquacopper(II) bis(sulfate)] with Zn leads to a change in the structure from dimorph A (low density) to dimorph B (high density). This change, which accompanies a switch in the direction of the Jahn-Teller distortion, had previously been observed to occur with substitution of Zn2+ at the Cu2+ site of between 1.3 (A) and 3.4% (B). In this study, the single-crystal neutron-diffraction analysis of (ND4)2[(Cu/Zn)(D2O)6](SO4)2 at 20 K, with 3.4% Zn doping and a deuterium substitution of 85% on the H-atom sites, reveals that the structure is entirely of type B, with the Cu/Zn site at an inversion centre and with no evidence of disorder or unusual atomic displacement parameters that might occur near a phase transition boundary.

Journal Article↗
PubMed2001

Direct observation of deuterium migration in crystalline-state reaction by single-crystal neutron diffraction. III. Photoracemization of 1-cyanoethyl cobaloxime complexes.

The H atoms bonded to the chiral C atoms (stereogenic center) of the 1-cyanoethyl groups in two cobalt complexes, [(R)-1-cyanoethyl]bis(dimethylglyoximato)(pyridine)cobalt(III) (2) and [(R,S)-1-cyanoethyl]bis(dimethylglyoximato)(piperidine)cobalt(III) (3), were replaced with D atoms, such as Co--C*D(CH(3))CN. The crystals of the two cobalt complexes were irradiated with a xenon lamp for 72 h and 27 d, respectively. The unit-cell dimensions were gradually changed with retention of the single-crystal form. The crystal structures after irradiation were determined by neutron diffraction. In each crystal the chiral 1-cyanoethyl group of one of the two crystallographically independent molecules was partly inverted to the opposite configuration, whereas that of the other molecule kept the original configuration. The C*--D bond in the inverted group was completely conserved in the process of the inversion of the chiral alkyl group. This suggests that the inversion of the chiral 1-cyanoethyl group proceeds with the rotation of the cyanoethyl radical after the Co--C bond cleavage by photo-irradiation so that the opposite side of the radical faces the Co atom. This is followed by recombination of the Co--C bond to form the inverted 1-cyanoethyl group.

Journal Article↗
PubMed2006

Neutron diffraction analysis of deuterium transfer in chiral beta-thiolactam formation in the crystalline state.

Since N,N-dibenzyl-1-cyclohexenecarbothioamide is photo-isomerized to the optically active beta-thiolactam with the retention of the single-crystal form, the mechanism of chirality induction was identified by X-ray crystal structure analyses during the process of the reaction [Hosoya et al. (2002). Bull. Chem. Soc. Jpn, 75, 2147-2151]. In order to clarify the mechanism of hydrogen transfer in the reaction, the H atoms of the benzyl groups were replaced with deuterium atoms. The crystal structure after photoisomerization was analyzed by neutron diffraction. One of four deuterium atoms of the two benzyl groups is transferred to the C atom of the cyclohexene ring. The absolute configuration of the -C*HD- group (chiral methylene) in the photoproduct beta-thiolactam revealed that the deuterium atom occupies the equatorial position. This suggests that the deuterium atom is not transferred from the benzyl group of a neighbouring molecule, but from one of the benzyl groups within the molecule.

Journal Article↗
PubMed2006

On hydrogen bonding in 1,6-anhydro-beta-D-glucopyranose (levoglucosan): X-ray and neutron diffraction and DFT study.

The geometry of hydrogen bonds in 1,6-anhydro-beta-D-glucopyranose (levoglucosan) is accurately determined by refinement of time-of-flight neutron single-crystal diffraction data. Molecules of levoglucosan are held together by a hydrogen-bond array formed by a combination of strong O-H...O and supporting weaker C-H...O bonds. These are fully and accurately detailed by the neutron diffraction study. The strong hydrogen bonds link molecules in finite chains, with hydroxyl O atoms acting as both donors and acceptors of hydroxyl H atoms. A comparison of molecular and solid-state DFT calculations predicts red shifts of O-H and associated blue shifts of C-H stretching frequencies due to the formation of hydrogen bonds in this system.

Crystallography, X-Ray↗
PubMed1984

Neutron diffraction of alpha, beta and gamma cyclodextrins: hydrogen bonding patterns.

Cyclodextrins (CD's) have proved useful as model systems for the study of hydrogen bonding. They are torus-shaped molecules composed of six(alpha), seven(beta) or eight(gamma) (1----4) linked glucoses. Because of their particular geometry, they are able to act as a "host" to form inclusion complexes with "guest" molecules very much like enzymes. Cyclodextrins have been shown to exert catalytic activity on suitable included-substrate molecules; they catalyze the hydrolysis of phenylacetates, of organic pyrophosphates and of penicillin derivatives. They also accelerate aromatic chlorinations and diazo coupling by means of their primary and/or secondary hydroxyl groups, so that the rates of hydrolysis are enhanced by up to a factor of 400. In order to understand the hydrogen bonding in these enzyme models, neutron diffraction data were collected to unambiguously determine the hydrogen atom positions, which could not be done from the x-ray diffraction data. alpha-CD has been shown to have two different structures with well-defined hydrogen bonds, one "tense" and the other "relaxed". An "induced-fit"-like mechanism for alpha-CD complex formation has been proposed. Circular hydrogen bond networks have also been found for alpha-CD due to the energetically favored cooperative effect. beta-CD with a disordered water structure possesses an unusual flip-flop hydrogen bonding system of the type O-H...H-O representing an equilibrium between two states: O-H...O in equilibrium O...H-O. gamma-CD with a disordered water structure similar to beta-CD also possesses the flip-flop hydrogen bond. This study demonstrates that hydrogen bonds are operative in disordered systems and display dynamics even in the solid state.

Crystallography↗
PubMed1963

SUCROSE: PRECISE DETERMINATION OF CRYSTAL AND MOLECULAR STRUCTURE BY NEUTRON DIFFRACTION.

This analysis provides the first precise molecular parameters for sucrose. All hydrogen atoms are included. Carbon-carbon distances are 1.51 1.53 A; carbon-oxygen 1.40 to 1.44 A; carbon-hydrogen 1.08 to 1.11 A; oxygen-hydrogen 0.94 to 0.99 A. The furanose ring conformation differs from that in sucrose sodium bromide dihydrate. Hydrogen bonds (two of them intramolecular) utilize every hydroxyl group except one.

Crystallography↗
PubMed2002

Isolation of the new cubic phases RE4FeGa(12-x)Ge(x) (RE = Sm, Tb; x = 2.5) from molten gallium: single-crystal neutron diffraction study of the Ga/Ge distribution.

The compounds RE4FeGa(12-x)Ge(x) (RE = Sm, Tb) were discovered in reactions employing molten Ga as a solvent at 850 degrees C. However, the isostructural Y4FeGa(12-x)Ge(x) was prepared from a direct combination reaction. The crystal structure is cubic with space group Imm, Z = 2, and a = 8.657(4) A and 8.5620(9) A for the Sm and Tb analogues, respectively. Structure refinement based on full-matrix least squares on F(o)2 resulted in R1 = 1.47% and wR2 = 4.13% [I > 2(I)] for RE = Sm and R1 = 2.29% and wR2 = 7.12% [I > 2(I)] for RE = Tb. The compounds crystallize in the U4Re7Si6 structure type, where the RE atoms are located on 8c (1/4, 1/4, 1/4) sites and the Fe atoms on 2a (0, 0, 0) sites. The distribution of Ga and Ge in the structure, investigated with single-crystal neutron diffraction on the Tb analogue, revealed that these atoms are disordered over the 12d (1/4, 0, 1/2) and 12e (x, 0, 0) sites. The amount of Ga/Ge occupying the 12d and 12e sites refined to 89(4)/11 and 70(4)/30%, respectively. Transport property measurements indicate that these compounds are metallic conductors. Magnetic susceptibility measurements and Mössbauer spectroscopy performed on the Tb analogue show a nonmagnetic state for Fe, while the Tb atoms carry a magnetic moment corresponding to a mu(eff) of 9.25 mu(B).

Journal Article↗