Showing papers by "Thomas F. Koetzle published in 1977"
TL;DR: The Protein Data Bank is a computer-based archival file for macromolecular structures that stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies.
7,983 citations
TL;DR: The Protein Data Bank is a computer-based archival file for macromolecular structures that stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies.
Abstract: The Protein Data Bank is a computer-based archival file for macromolecular structures. The Bank stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies. Text included in each data entry gives pertinent information for the structure at hand (e.g. species from which the molecule has been obtained, resolution of diffraction data, literature citations and specifications of secondary structure). In addition to atomic co-ordinates and connectivities, the Protein Data Bank stores structure factors and phases, although these latter data are not placed in any uniform format. Input of data to the Bank and general maintenance functions are carried out at Brookhaven National Laboratory. All data stored in the Bank are available on magnetic tape for public distribution, from Brookhaven (to laboratories in the Americas), Tokyo (Japan), and Cambridge (Europe and worldwide). A master file is maintained at Brookhaven and duplicate copies are stored in Cambridge and Tokyo. In the future, it is hoped to expand the scope of the Protein Data Bank to make available co-ordinates for standard structural types (e.g. alpha-helix, RNA double-stranded helix) and representative computer programs of utility in the study and interpretation of macromolecular structures.
581 citations
TL;DR: A neutron diffraction study of squaric acid (C4H2O4; 3,4−dihydroxy−3,cyclobutene•1,2−dione) at 25°C has been carried out.
Abstract: A neutron diffraction study of squaric acid (C4H2O4; 3,4‐dihydroxy‐3‐cyclobutene‐1,2‐dione) at 25°C has been carried out. Space group P21/m, a=6.143(2), b=5.286(2), c=6.148(2) A, β=89.96(2) °, Z=2. The structure has been refined with 67 variable parameters on 1026 reflections, comprising one hemisphere of the reciprocal lattice to yield a conventional crystallographic R value of 0.025. An anisotropic extinction correction was applied, and 66 reflections severely effected by extinction were not used in the final cycles of refinement. The squaric acid molecules are linked by strong hydrogen bonds to form infinite planar layers in the crystallographic mirror planes. The hydrogen bond lengths are H⋅⋅⋅O 1.034 and O⋅⋅⋅O 2.554 A, the O−H⋅⋅⋅O angle is 177.5°. Average intramolecular bond distances are C–O 1.288, C=O 1.229, C–C 1.500 and 1.462, and C=C 1.414 A.
128 citations
TL;DR: In this paper, the molecular structures of H/sub 3/Nb(C/sub 5/H/Sub 5/)/sub 2/ ) and isoelectronic compounds were analyzed by x-ray and neutron diffraction techniques, respectively.
Abstract: The molecular structures of H/sub 3/Nb(C/sub 5/H/sub 5/)/sub 2/ and H/sub 3/Ta(C/sub 5/H/sub 5/)/sub 2/ have been analyzed by x-ray and neutron diffraction techniques, respectively. In both compounds the central H/sub 3/M fragment is planar within experimental error and defines a noncrystallographic mirror plane for the molecule. The three hydridic atoms are essentially equidistant from the metal atom and are arranged with the central M--H bond in a bisecting position. From the x-ray diffraction analysis of H/sub 3/Nb(C/sub 5/H/sub 5/)/sub 2/, Nb-H = 1.65 (6), 1.65 (6), and 1.76 (7) A, and H-Nb-H = 65 (3) and 61 (3)/sup 0/. More accurate distances and angles were obtained from the neutron diffraction analysis of H/sub 3/Ta(C/sub 5/H/sub 5/)/sub 2/: Ta-H = 1.769 (8), 1.775 (9) A; H-Ta-H = 62.8 (5) and 63.0 (4)/sup 0/. Other important molecular parameters are as follows: for H/sub 3/Nb(C/sub 5/H/sub 5/)/sub 2/, Nb-ring (centroid) = 2.059 A, Nb-C (av) = 2.375 A, ring-Nb-ring bending angle = 141.6/sup 0/; for H/sub 3/Ta(C/sub 5/H/sub 5/)/sub 2/, Ta-ring = 2.065 A, Ta-C(av) = 2.393 A, ring-Ta-ring bending angle = 139.9/sup 0/. The structure of the isoelectronic compound (H/sub 3/W(C/sub 5/H/sub 5/)/sub 2/)/sup +/Cl/sup -/ has also been examined, andmore » found to be similar to that of H/sub 3/Nb(C/sub 5/H/sub 5/)/sub 2/ and H/sub 3/Ta(C/sub 5/H/sub 5/)/sub 2/. Final agreement factors (based on F) for data with I greater than 3 sigma:in H/sub 3/Nb(C/sub 5/H/sub 5/)/sub 2/, R/sub F/ = 0.035 and R/sub wF/ = 0.043 for 1530 reflections (x-ray data collected at room temperature); in H/sub 3/Ta(C/sub 5/H/sub 5/)/sub 2/, R/sub F/ = 0.069 and R/sub wF/ = 0.051 for 841 reflections (neutron data collected at 90 K).« less
90 citations
TL;DR: The molecular and crystal structure of squaric acid (3,4−dihydroxy−3,cyclobutene•1,2−dione) has been determined by neutron diffraction techniques at 121°C, a temperature above that of the monoclinic to tetragonal phase transition (∼100°C) as mentioned in this paper.
Abstract: The molecular and crystal structure of squaric acid (3,4‐dihydroxy‐3‐cyclobutene‐1,2‐dione) has been determined by neutron diffraction techniques at 121°C, a temperature above that of the monoclinic to tetragonal phase transition (∼100°C). The high‐temperature structure is in space group I4/m, a=c=6.137(2) A, b=5.337(2) A. Least‐squares refinement has been carried out with 25 variable parameters and 276 reflections, to yield an unweighted R value (on F2) of 0.042. The squaric acid molecule has point symmetry 4/m, and the hydrogen atom is ’’disordered’’ about the inversion center at the midpoint of the O⋅⋅⋅O hydrogen bond. Hydrogen‐bonding parameters are O–H 1.014(4), H⋅⋅⋅O 1.536(5) A, O⋅⋅⋅O 2.548(2) A, & O–H⋅⋅⋅O 176.2(6) °. The tetragonal structure corresponds closely to that obtained from the atomic parameters determined in the monoclinic phase at 25°C, by averaging over the pseudofourfold symmetry.
73 citations
47 citations
TL;DR: The crystal and molecular structure of H/sub 4/Os(PMc/sub 2/Ph)/sub 3/ has been investigated by x-ray and neutron diffraction technijues as discussed by the authors.
Abstract: The crystal and molecular structure of H/sub 4/Os(PMc/sub 2/Ph)/sub 3/ has been investigated by x-ray and neutron diffraction technijues. X-ray data collected at 298 K gave the unit cell parameters a = 11.489 (4) A, b = 12.441 (4) A, c = 11.103 (4) A, ..cap alpha.. = 90.54 (2)/sup 0/, ..beta.. = 124.63 (2)/sup 0/, ..gamma.. = 89.93 (2)/sup 0/, Z = 2 in the triclinic space group P anti 1. Neutron data collected at 90 K gave the cell parameters a = 11.409 (2) A, b = 12.388 (2) A, c = 11.098 (2) A, ..cap alpha.. = 90.36 (5)/sup 0/, ..beta.. = 125.07 (1)/sup 0/, and ..gamma.. = 90.06 (4)/sup 0/. Refinement against the x-ray data coverged at R = 0.055 and R/sub w/ = 0.060 with 3486 reflections with 1 greater than or equal to 30. For the neutron study, agreement factors are R = 0.044 and R/sub w/ = 0.042 based on 3381 reflections. The complex is a distorted pentagonal bipyramid, the four hydride ligands, osmium, and one phosphorus atom being essentially coplanar. Important distances and angles in the molecule are as follows: Os-H = 1.663 (3), 1.648, 1.644 (3), 1.681 (3) A; Os-P =more » 2.317 (2), 2.307 (2), 2.347 (2) A; H-Os-H = 67.9 (2), 69.4 (2), 70.0 (2)/sup 0/; P-Os-P = 166.1 (1), 97.0 (1), 96.9 (1)/sup 0/; H-Os-P(eq) = 73.0 (1), 79.7 (1)/sup 0/.« less
43 citations
Journal Article•
TL;DR: The molecular structures of four transition metal polyhydride complexes are reported, H/sub 3/Ir(PMe/sub 2/Ph)/sub 3/, H/Sub 7/Re(Pme/sub 1/P)/sub 2), and H/ Sub 8/Re/sub 4/dimer by neutron diffraction analysis as mentioned in this paper.
Abstract: The molecular structures of four transition metal polyhydride complexes are reported, H/sub 3/Ir(PMe/sub 2/Ph)/sub 3/ and H/sub 7/Re(PMe/sub 2/Ph)/sub 2/ by x-ray diffraction analysis and H/sub 4/Os(PMe/sub 2/Ph)/sub 3/ and H/sub 8/Re/sub 2/(PEt/sub 2/Ph)/sub 4/ by neutron diffraction analysis. Although the hydride ligands were not located in H/sub 3/Ir(PMe/sub 2/Ph)/sub 3/, the arrangement of phosphorus atoms about the Ir atom (average distance = 2.294(3)A, average P-Ir-P angle = 101.0(1)/sup 0/) suggests a distorted octahedral geometry for this molecule. The x-ray analysis of H/sub 7/Re(PMe/sub 2/Ph)/sub 2/ revealed a bent P-Re-P backbone for the molecule (P-Re-P angle = 146.8(1)/sup 0/), which is consistent with a tricapped trigonal prism with P atoms in equatorial positions. The neutron diffraction analysis of H/sub 4/Os(PMe/sub 2/Ph)/sub 3/ shows that the molecule is a distorted pentagonal bipyramid, with one equatorial and two axial phosphine ligands (P-Os-P angles are 166.07(8)/sup 0/, 97.08(7)/sup 0/, and 96.85(8)/sup 0/). Pertinent distances and angles within the planar H/sub 4/OsP group are: Os-H, 1.663(3), 1.648(3), 1.644(3), and 1.681(3)A; H-Os-H, 69.4(2)/sup 0/, 69.7(2)/sup 0/, and 70.0(2)/sup 0/; H-Os-P, 79.7(1)/sup 0/ and 73.0(1)/sup 0/. The neutron diffraction analysis of the H/sub 8/Re/sub 2/(PEt/sub 2/Ph)/sub 4/ dimer reveals a molecule with four terminal and fourmore » bridging hydride ligands. This molecule provides the first example of a metal-metal bond bridged by four hydrogen atoms. Some distances and angles are: Re-H(terminal), 1.682(7) and 1.656(7)A; Re-H(bridging), 1.882(7), 1.862(7), 1.885(7), and 1.883(8)A; Re-H-Re, 85.4(3)/sup 0/ and 84.7(3)/sup 0/.« less
4 citations