Difference Electron Density Map Research Articles

A chloride of a substituted heterocyclic analogue of chrysene: C19H17N2O+.Cl−

thermal parameters for the H atoms were fixed throughout all subsequent refinements. Least-squares refinement converged to final R = 0.044, wR = 0.048, S = 1.416. At this point all subsequent shifts were found to be < 0.001tr. A single prominent peak is evident on the difference electron density map measuring 0.67 e A -3 in the immediate vicinity of Br. Otherwise, all remaining difference peaks were found to be < 0.39 e A -3. Anomalous scattering of Br anti S atoms was employed for verification of the proper choice of enantiomeric configuration, following the statistical criterion proposed by Hamilton (1965). The opposite enantiomorph refined to final reliability indices of R = 0.051, wR = 0.057. Scattering factors for neutral atoms and anomalous-scattering parameters for Br and S atoms were taken from International Tables for X-ray Crystallography (1974, Vol. IV). All calculations were performed on a PDP 11/60 utilizing the SDP-Plus package (Frenz, 1978). Discussion. Refined positional parameters for all atoms and equivalent isotropic B values are supplied in Table 1. Atom numbering follows the scheme indicated in Fig. 1. Fig. 2 shows a stereo OR TEP (Johnson, 1976) representation of the molecule. Interatomic bonding distances and angles are supplied in Table 2.* Bond distances and angles are, generally, as expected. The one exception to this is * Lists of structure factors, complete bond distances and angles, and anisotropic thermal parameters have been deposited with the British Library Document Supply Centre as Supplementary Publication No. SUP 55634 (18 pp.). Copies may be obtained through The Technical Editor, International Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England. [CIF reference: CRI012]

Structure of a rhombohedral R6 insulin/phenol complex.

Hexameric insulin has been crystallized from different conditions in a variety of crystalline modifications. In the presence of approximately 1% phenol and at a pH of 8.5, a new rhombohedral form is produced, space group R3, a = 79.92A and c = 40.39A, in which the asymmetric unit consists of a dimer. The structure has been solved and refined, using data between 8.0 and 2.5A resolution, to a residual of 0.157. The two monomers in the asymmetric unit have nearly identical R conformations, that is, residues B1 through B8 are alpha-helical, producing a continuous alpha-helix from B1 through B19. A phenol molecule is hydrogen bonded to the carbonyl oxygen of A6 Cys of each monomer. Small differences in conformation and the final (2Fo-Fc) and difference electron density maps suggest that an additional phenol molecule is coordinated to one of the two zinc ions.

X-ray diffraction study of di and tetra-ligated T-state hemoglobin from high salt crystals

X-ray diffraction difference electron density maps at 3 Å resolution obtained from di and tetra-ligated T-state hemoglobin (Hb) crystals are reported. Crystals isomorphous with native deoxyhemoglobin were obtained from ammonium sulfate solutions incubated with the synthetic allosteric effector RSR-56. RSR-56 binds at two symmetry-related Hb central water cavity sites and each molecule has major interactions with three different subunit side-chains; one effector with Arg141α2 HC3, Lys99α1 G6 and Asn108β1 and the other with the symmetry related residues, Arg141α1 Lys99α2 and Asn108β2. Crystals mounted in a nitrogen filled glove box were di-ligated as previously found with polyethyleneglycol Hb crystals. Crystals mounted in air under a layer of mother liquor were bright red and showed all four heme groups ligated. The difference electron density from the di-ligated crystals showed atomic movements to be restricted to the immediate neighborhood of the heme groups and the allosteric effector. By contrast, the tetra-ligated structure showed extended difference electron density near amino acid residues around both α and β heme groups and along the α1 β2 interface. Ligation of the β heme group appears to magnify the difference density around the α heme groups. There is no evidence of breakage of the Bohr salt bridge, His146β HC3 → Asp94β FG1, in the crystal. The observed difference electron density maps may help to clarify the way the allosteric mechanism is triggered.

Structure determination of the bacteriophage phiX174.

The structure of the single-stranded DNA phage phiX174 has been determined to 3.4 A resolution. The crystal space group was P2(1) with one icosahedral particle per asymmetric unit, giving 60-fold noncrystallographic redundancy. Oscillation diffraction photographs were collected using synchrotron radiation at various wavelengths. The particle orientations in the unit cell were determined with a rotation function. Because cowpea mosaic virus has a similar external envelope to phiX174, it was used as a search model to find the approximately positions of the phiX174 particles in the unit cell relative to the crystallographic symmetry axes. An initial phase set to 12 A resolution was then based on the cowpea mosaic virus atomic structure. These phases were improved by 20 cycles of real-space molecular replacement averaging. The phase information was gradually extended to 3.4 A resolution by molecular replacement electron density averaging. One reciprocal lattice point was used for each extension followed by four cycles of averaging. The unusual particle capsid, with its 12 pentameric spikes, required the careful determination of a precise molecular envelope. This was redetermined at regular intervals, as was the particle center. The resultant electron density map was readily interpreted in terms of the F, G and J polypeptides in the capsid. A difference electron density map between full and partially empty particles showed some ordered DNA structure.

Crystal structure of an electron-transfer complex between methylamine dehydrogenase and amicyanin.

The crystal structure of the complex between the quinoprotein methylamine dehydrogenase (MADH) and the type I blue copper protein amicyanin, both from Paracoccus denitrificans, has been determined at 2.5-A resolution using molecular replacement. The search model was MADH from Thiobacillus versutus. The amicyanin could be located in an averaged electron density difference map and the model improved by refinement and model building procedures. Nine beta-strands are observed within the amicyanin molecule. The copper atom is located between three antiparallel strands and is about 2.5 A below the protein surface. The major intermolecular interactions occur between amicyanin and the light subunit of MADH where the interface is largely hydrophobic. The copper atom of amicyanin and the redox cofactor of MADH are about 9.4 A apart. One of the copper ligands, His 95, lies between the two redox centers and may facilitate electron transfer between them.

The crystal structure of SeO2at 139 and 286 K

The structural model of tetragonal SeO 2 proposed by McCullough [JACS 59 (1937) 789] has been refined at 139 and 286 K. Space group P 4 2 / mbc , Z = 8, M w = 110.96, a = 8.3218(9), c = 5.0541(6) Å, V = 350.0(1) Å 3 at 139 K and a = 8.3622(7), c = 5.0612(5) Å, V = 353.9(1) Å 3 at 286 K. 349 and 635 unique reflections refined to R ( F ) = 0.023 and 0.019 at 139 and 286 K, respectively. The structure consists of infinite chains along c , built from corner sharing SeO 3 E tetrahedra, with E representing the Se lone pair. Observed bonding distances are Se–O(1) (*2) 1.7926(4) [1.795(1)] and Se–O(2) 1.6226(9) [1.624(2)] Å at 286 [139] K. The shortest inter-chain distances, Se---O(2) 2.758(1) [2.743(2)] and (*2) 2.857(1) [2.843(1)] Å at 286 [139] K, indicate considerable electrostatic interactions between chains. Including these next nearest oxygens the Se–O coordination can be described as distorted octahedral in a novel type of net. The final difference electron density map showed residual density in the predicted Se lone pair region.

Structure of 2-oxo-4-thiazolidinecarboxylic acid

C4HsNO3S , Mr = 147.15, orthorhombic, P212~2~, a = 5.968 (3), b = 17.945 (3), c = 5.387 (3) A, V= 576.9 (4) A 3, Z = 4, Ox = 1.69 g cm -3, a(Mo Ka) = 0.71069 ,~,/.i, = 4.63 cm-~, F(000) = 304, T = 296 K, R = 0.034 for 730 reflec- tions with I > 2.500-(/). Hydrogen bonds NH...O z C(carboxyl) 2.96 and OH...OzC(carbony l) 2-62 A afford a sheet structure. A signal 4-4 times that of quartz is observed in an optical second-harmonic test. Introduction. The methyl ester of the title compound was prepared as an intermediate in the total synthesis of latrunculin A (White & Kawasaki, 1990). The hydrolyzed ester contains a high density of chromo- phores of interest for optical frequency conversion at short wavelengths and so crystals were grown to determine the structure and efficiency of second- harmonic generation. Experimental. The compound was obtained by acid hydrolysis of the corresponding methyl ester fol- lowing a known procedure (Maclaren, 1968). Crys- tals were grown by slow evaporation of an aqueous solution. A block of dimensions 0-25 × 0.30 × 0.25 mm was mounted on a glass fiber and used for collection of data on a Rigaku AFC6R diffractom- eter. Unit-cell parameters were refined by least- squares analysis of the angle settings of 16 reflections in the range 30.5 2-5o'(1) were obtained. All calculations were performed on a MicroVAX II computer with programs from the TEXSAN crys- tallographic software package (Molecular Structure Corporation, 1989). Atomic scattering factors were taken from International Tables for X-ray Crystallog- raphy (1974, Vol. IV). Atomic positions were obtain- 0108-2701/91/071481-02503.00 ed using the direct-methods program MITHRIL (Gilmore, 1984). H atoms bound to C atoms were placed in calculated positions (C--H = 0.95 A) and assigned isotropic thermal parameters of 1.5 x Beq of the associated C atom. The remaining H atoms were located in a difference electron density map. Posi- tional parameters and the isotropic thermal param- eter were subsequently refined for each of these H atoms. Minimization of the function Zw(Fo- Fc) 2 (where w = 1/0.2(Fo)) with those data having I> 2.50(/) using 90 variables and 730 observations affords the residuals R = 0.034, wR = 0-045 and the indicator S = 1-79. In the final cycle of refinement A/0.=0.01. The maximum feature in the final difference electron density map was 0.21 e/~-3. The enantiomorphs are indistinguishable from the X-ray data. Fractional atomic coordinates and isotropic temperature coefficients are given in Table 1.*

Cis-trans isomerization of protonated formaldehyde and its fluoro and chloro substituents

The cis-trans isomerization of protonated carbonyl compounds' can take place through a planar or a torsional pathway. Protonated formaldehyde serves as the simplest model for these processes, and was studied in detail at the 4–31G level with the aid of electron density difference maps and population analysis. The mechanism and energetics of both pathways were studied via their transition states. The structural changes that take place during the isomerization process were correlated with the electron density migration accompanying the isomerization. The energy barriers for isomerization of the protonated species of formaldehyde and its fluoro and chloro substituted analogues (HFCO, F 2CO, HClCO, Cl 2CO and FClCO), were calculated. The planar pathway is energetically preferred over the torsional pathway in all the molecules studied.

X-ray diffraction study of the binding of the antisickling agent 12C79 to human hemoglobin.

The hemoglobin binding site of the antisickling agent 12C79 has been determined by x-ray crystallography. 12C79 is recognized as one of the first molecules to reach clinical trials that was designed, de novo, from x-ray-determined atomic coordinates of a protein. Several previous attempts to verify the proposed Hb binding sites via crystallographic studies have failed. Using revised experimental procedures, we obtained 12C79-deoxyhemoglobin crystals grown after reaction with oxyhemoglobin and cyanoborohydride reduction to stabilize the Schiff base linkage. The difference electron-density Fourier maps show that two 12C79 molecules bind covalently to both symmetry-related N-terminal amino groups of the hemoglobin alpha chains. This is in contrast to the original design that proposed the binding of one drug molecule that spans the molecular dyad to interact with both N-terminal alpha-amino groups.

An Improved Synthesis, Molecular-Structure, and Properties of 1,4-Dihydro-Dicyclopropa[b,g]naphthalene

A marked improvement in the preparation of 1,4-dihydrodicyclopropa[ b,g ]naphthalene (4) from isotetralin (7) has been achieved by selecting conditions which avoid the unwanted olefin (12). The easily available dicycloproparene (4) has C2h symmetry in the crystal lattice with the space group P21/n. The geometry is readily rationalized by the concept of 'bent bonds' that are also suggested by X-X difference electron density maps. Cheletropic biaddition of dichlorocarbene to (4) provides the dicyclobutanaphthalenes (15) and (16). Attempted Petersen olefination to mono- and di-alkylidene derivatives, e.g. (21) and (22), is foiled by a reluctance of (4) to provide an easily interceptible anion.

Experimental distinction of elements with similar atomic number using anomalous dispersion (δ synthesis): an application of synchrotron radiation in crystal structure analysis

A two-wavelength method (δ synthesis) which deals with the experimental distinction of elements with similar atomic number by means of single-crystal X-ray diffraction measurements is presented. This method uses the characteristic wavelength dependence of the anomalous-dispersion correction terms f′ and f′′ close to the absorption edges of the corresponding elements. In case of a properly chosen wavelength combination the resulting difference electron density map (δ map) mainly shows peaks at the positions of the 'near-edge' element. The basic mathematical formalism is described and selection rules for the determination of the optimal wavelength combination are derived. The applicability in case of mixed occupancy and/or occupancy deficiency is discussed. A series of δ maps which are based on theoretical data sets and calculated according to the formalism of the δ synthesis are shown. From this the influence of errors on the interpretation of the δ map can be estimated and the requirements on the experimental conditions can be determined. First experimental results concerning the distinction of Pb/Bi in the well known crystal structure of galenobismutite (PbBi2S4) are presented. They show that the δ synthesis is not only a theoretical model, but can be applied successfully in practice. For experimental reasons the applicability of the δ synthesis is restricted to elements with atomic numbers greater than Z = 22.

Erdalkaliquadratate, VII [1] Eine neue Koordinationsvariante des Quadratatdianions in BeC4O4· 3H2O / Alkaline-Earth Squarates, VII [1] A New Coordination Mode of the Squarate Dianion in BeC4O4· 3 H2O

Single crystals of BeC4O4 · 3 H2O were prepared from aqueous solution. The X-ray structure determination revealed a new coordination mode of the squarate dianion. C4O4 2- is bound to Be2+ by only one of its oxygen atoms. Three water molecules join the Be coordination sphere to form a slightly distorted tetrahedron together with the Osquarate atom. Be-Osquarate bond lengths are negligibly shorter than Be—OH2 distances. Strong hydrogen bonds occur between water molecules and all Οsquarate atoms not bound to Be2+. These Osquarate atoms act as proton acceptors in two hydrogen bonds, each of almost equal strength. One intramolecular hydrogen bond occurs within the BeC4O4.3 H2O moieties which are connected to each other by intermolecular hydrogen bonds. C4O4 2- does not deviate markedly from planarity. Difference electron density maps show evidence for bent bonds in the C4 ring system of C4O4 2-.

BYPASS: an effective method for the refinement of crystal structures containing disordered solvent regions

A method is described for the least-squares refinement of the atomic parameters of the ordered part of a crystal structure in the presence of disordered solvent areas. Potential solvent regions are identified automatically. The contribution of the observed contents to the total structure factor is calculated via a discrete Fourier transformation, and incorporated in a further least-squares refinement of the ordered part of the structure. The procedure is iterated a few times to convergence. It is found that this mixed discrete-atom and continuous solvent-area model refinement approach greatly improves the quality of discrete atomic parameters, i.e. the geometry and the e.s.d.'s. An electron count over the solvent region in the final difference electron-density map provides a convenient estimate for the number of solvent molecules present in the unit cell. The application of the method to four structures is described.

Crystal structure of a papain-E-64 complex.

E-64 [1-[N-[(L-3-trans-carboxyoxirane-2-carbonyl)-L-leucyl] amino]-4-guanidinobutane] is an irreversible inhibitor of many cysteine proteases. A papain-E-64 complex was crystallized at pH 6.3 by using the hanging drop method. Three different crystal forms grew in 3-7 days; the form chosen for structure analysis has space group P212121, with a = 42.91(4) A, b = 102.02(6) A, c = 49.73(2) A, and Z = 4. Diffraction data were measured to 2.4-A resolution, giving 9367 unique reflections. The papain structure was solved by use of the molecular replacement method, and then the inhibitor was located from a difference electron density map and fitted with the aid of a PS330 computer graphics system. The structure of the complex was refined to R = 23.3%. Our analysis shows that a covalent link is formed between the sulfur of the active-site cysteine 25 and the C-2 atom of the inhibitor. Contrary to earlier predictions, the E-64 inhibitor clearly interacts with the S subsites on the enzyme rather than the S' subsites, and papain's histidine 159 imidazole group plays a binding rather than a catalytic role in the inactivation process.

Embedded cluster models for electronic structure and energetics of complex oxides

Electronic structures and energetics of complex oxide systems have been investigated using the self-consistent embedded cluster model in the framework of local density theory. Ground state charge and spin distributions and energy level diagrams are generated for perfect host lattices, and for vacancy and impurity environments. The polarization response of perfect and defect lattices is explored by performing self-consistent calculations in the presence of an external electric field. Electron density difference maps are used to display local changes in electron distributions induced by vacancies, cation substitution, and external electric fields. Local multipolar moments are determined for quantitative analysis of the response of the system to the induced disturbances. Cohesive energies are calculated for molecular fragments, and are used to study relative energetics of the perfect host lattices and various defect structures with and without external electric field. Results obtained from oxide systems with NaCl-type structure, as well as rare-earth and alkali-earth stabilized cubic zirconia and superconducting La 2CuO 4, will be presented and discussed.

Is the Isotropic Atom—Atom Model Potential Adequate?

Abstract We discuss some of the problems that have frustrated the development of reliable model intermolecular potentials for polyatomic molecules. In particular, the usual assumption of an isotropic atom-atom model potential is analysed, and evidence for its inadequacies is presented. A new approach to designing model potentials, an anisotropic site—site model, is introduced by describing several applications to both small and organic molecules, including molecular dynamics and Monte Carlo simulations. The anisotropy required in an atom—atom potential can be directly linked to the non-spherical features in the valence electron distribution, such as lone pairs and π electrons. An accurate electrostatic model for these effects can be constructed from a distributed multipole analysis of the ab initio wavefunction. The empirically required forms of anisotropy in the repulsion potential can also be qualitatively linked to the molecular electron density difference map. Thus, consideration of the molecular bond...

Conjugative effects in furan syn-diepoxides. Crystal and molecular structure of methyl 3,5,7-trioxatricyclo[4.1.0.0] heptane-1-carboxylate

The stereochemistry of the title compound (2), a furan diepoxide derivative, has been defined in detail by means of an X-ray crystal structure analysis. Triclinic crystals in space group P have lattice parameters a= 4.1979(4), b= 13.948(1), c= 5.7324(4)A, α= 92.462(7), β= 103.070(7), γ= 91.136(8)°, and Z= 2. The structure was solved by direct methods and refined by full-matrix least-squares calculations to R= 0.048 with 948 observed reflections. The two epoxy rings are in syn configuration, the five-membered ring is strictly planar and there are evidences of a π electron conjugation between the epoxy rings through a 2p orbital of the interconnecting oxygen atom. A suggestion for the interpretation of the reaction of crystal decay has been provided by the scrutiny of the difference electron density map.

Electron-density distribution in ilmenite-type crystals. III. Nickel(II) titanium(IV) trioxide, NiTiO3.

The electron-density distribution in a crystal of NiTiO3 has been investigated by means of the single crystal X-ray diffraction method. A small amount of partial disorder was observed in the cation arrangement of the examined crystal. The difference electron-density maps showed an aspherical distribution of 3d electrons of the Ni2+ ion in the octahedral crystal field. Electron populations of the a, e(t2g) and e(eg) orbitals of Ni2+ were refined on the basis of the 3(C3) crystal field, employing aspherical scattering factors for the cation. The refinement gave the populations 1.84(9), 4.00(10) and 2.16(7) for the respective orbitals. The Ti4+ ion lies in a negative region of the difference Fourier map after the spherical atom refinement, and a positive peak exists on the threefold axis at a position 0.49 A apart from the Ti4+ ion towards the Ni2+ ion. These residual densities around Ti4+ are supposed to be caused by positive charge of the neighbouring Ni2+ ion. A residual peak is also observed at the middle of the neighbouring Ni2+ and Ti4+ along the threefold axis, which might be an indication of a metal-metal bonding. Refinements with anharmonic thermal parameters for the cations, up to the fourth order, revealed that anharmonicity is small at the room temperature in the present crystal.

Crystal structure of the trigonal form of bovine beta-lactoglobulin and of its complex with retinol at 2.5 A resolution.

The structure of the trigonal crystal form of bovine beta-lactoglobulin has been determined by X-ray diffraction methods. An electron density map, calculated with phases obtained by the multiple isomorphous replacement method, served as a starting point for alternate cycles of model building and restrained least-squares refinement. The model of the molecule fitted to the initial Fourier map was the one built for the orthorhombic crystal form of beta-lactoglobulin, solved at 2.8 A resolution (1 A = 0.1 nm). The final R factor for 1456 atoms (1276 non-hydrogen protein atoms and 180 solvent atoms) is 0.22, including 5245 reflections from 6.0 to 2.5 A. The molecule shows significant differences in the two crystal forms mentioned, mainly due to different packing. In the trigonal form, the species crystallized does not appear to be dimeric, but a linear polymer with tight intermolecular contacts. A difference electron density map between the complex of beta-lactoglobulin with retinol and the native protein shows no significant peaks in the cavity which, in the similar retinol-binding protein, binds the chromophore. Instead, differences are found at a surface pocket, which is limited almost completely by hydrophobic residues.

Structure of porcine heart cytoplasmic malate dehydrogenase: combining X-ray diffraction and chemical sequence data in structural studies.

The amino acid sequence of cytoplasmic malate dehydrogenase (sMDH) has been determined by a combination of X-ray crystallographic and chemical sequencing methods. The initial molecular model incorporated an "X-ray amino acid sequence" that was derived primarily from an evaluation of a multiple isomorphous replacement phased electron density map calculated at 2.5-A resolution. Following restrained least-squares crystallographic refinement, difference electron density maps were calculated from model phases, and attempts were made to upgrade the X-ray amino acid sequence. The method used to find the positions of peptides in the X-ray structure was similar to those used for studying protein homology and was shown to be successful for large fragments. For sMDH, X-ray methods by themselves were insufficient to derive a complete amino acid sequence, even with partial chemical sequence data. However, for this relatively large molecule at medium resolution, the electron density maps were of considerable help in determining the linear position of peptide fragments. The N-acetylated polypeptide chain of sMDH has 331 amino acids and has been crystallographically refined to an R factor of 19% for 2.5-A resolution diffraction data.