Hakon Hope

XABS2: an empirical absorption correction program

The XABS2 Fortran program calculates an empirical absorption correction based on minimization of the 2 differences between F2obs and F2calc. The basic algorithm has been used in the crystallography laboratory at the University of California, Davis for over a decade, in the form of the program XABS. XABS relied upon an approximately linear relationship for spherical crystals between the transmission factor and sin2 θ for θ ≃ 30° when μR ≃ 5. In XABS2, deviations from linearity are accounted for by a cubic equation in sin2 θ, which makes it applicable over the whole range of diffraction angle. The program needs no data in addition to the unique set but assumes a bisecting (symmetric) data-collection mode on a four-circle diffractometer. Since it does not require knowledge of the diffractometer setting angles, it can be applied even in cases where details of the original data collection are unknown.

Alkaloids from the antarctic sponge Kirkpatrickia varialosa. : Part 1: Variolin b, a new antitumour and antiviral compound

Abstract Variolin B (1), a new type of pyridopyrrolopyrimidine alkaloid with antitumour and antiviral properties, has been isolated from the Antarctic sponge Kirkpatrickia varialosa, and its structure determined by X-ray crystallography. A degradation product, variolin D (2), has been identified from its spectroscopic data.

Macromolecular Cryocrystallography: Cooling, Mounting, Storage and Transportation of Crystals

Simple methods are presented for handling, mounting, storage and transportation of crystals at cryogenic temperatures. They are easy to learn and have a number of technical and operational advantages over currently popular methods. In particular, the temperature of the crystal throughout all manipulations is known; it is shown never to rise above that of the warmest component of the cryogenic system, typically the cold gas stream of the low-temperature apparatus. Crystals can be mounted and inspected in the home laboratory prior to transportation to a synchrotron, giving dramatic savings in experimental time and effort. Provided appropriate care is taken, crystals remain frost free throughout any number of mount–dismount cycles.

Structure of bovine pancreatic trypsin inhibitor at 125 K definition of carboxyl-terminal residues Gly57 and Ala58.

The structure of bovine pancreatic trypsin inhibitor has been refined to a resolution of 1.1 A against data collected at 125 K. The space group of the form II crystal is P2(1)2(1)2(1) with a = 75.39(3), b = 22.581(7), c = 28.606 (9) A (cf. a = 74.1, b = 23.4, c = 28.9 A at room temperature). The structure was refined by restrained least-squares minimization of summation operator w(F (o)(2)- F (c)(2))(2) with the SHELXL93 program. As the model improved, water molecules were included and exceptionally clear electron density was found for two residues, Gly57 and Ala58, that had been largely obscured at room temperature. The side chains of residues Glu7 and Arg53 were modelled over two positions with refined occupancy factors. The final model contains 145.6 water molecules distributed over 167 sites, and a single phosphate group disordered over two sites. The root-mean-square discrepancy between Calpha atoms in residues Arg1-Gly56 at room and low temperatures is 0.4 A. A comparison of models refined with anisotropic and isotropic thermal parameters revealed that there were no significant differences in atomic positions. The final weighted R-factor on F(2) (wR(2)) for data in the range 10-1.1 A was 35.9% for the anisotropic model and 40.9% for the isotropic model. Conventional R-factors based on F for F > 4sigma(F) were 12.2 and 14.6%, respectively, corresponding to 16.1 and 18.7% on all data. These large R-factor differences were not reflected in values of R(free), which were not significantly different at 21.5(5) and 21.8(4)%, respectively. These results, along with the relatively straightforward nature of the refinement, clearly highlight the benefits of low-temperature data collection.

THE SYNTHESIS AND STRUCTURE OF TWO FILLED SKUTTERUDITE COMPOUNDS : BAFE4SB12 AND BARU4SB12

Abstract Two compounds, BaT4Sb12 (T = Fe, Ru), have been synthesized using high temperature methods. These compounds crystallize in the cubic LaFe4P12 structure type. Two methods are described for the synthesis of BaFe4Sb12. Single crystals of BaFe4Sb12 can be prepared by reacting BaSb, Fe, and Sb in a 1:4:18 (Ba:Fe:Sb) molar ratio (method I). Single crystal X-ray diffraction data (room temperature, a = 9.200(3) A) for BaFe4Sb12 prepared by Method I were refined (cubic, Im 3 (No. 204), Z = 2, R = 1.96%, Rw = 1.73% for 179 independent reflections). BaFe4Sb12 can also be prepared in ≥80% yield from the reaction of stoichiometric amounts of Ba2Sb3, FeSb2, and Sb (method II). Low temperature (130 K, a = 9.188(2)) single crystal X-ray diffraction data on BaFe4Sb12 crystals produced from Method II were also measured and refined (R = 2.29%, Rw = 2.45% for 179 independent reflections). The structure of BaFe4Sb12 will be compared to that of the LaFe4Sb12 and CoSb3.

Addition of tin(II) chloride to Pd2(Ph2PCH2PPh2)2CI2. The crystal and molecular structure of Pd2(Ph2PCH2PPh2)2(SnCl3)Cl

Abstract Addition of tin(II) chloride to Pd2(dpm)2Cl2 (dpm is Ph2PCH2PPh2) produces Pd2(dpm)2(SnCl3)Cl. The crystal structure of the latter complex reveals that the tin(II) chloride has inserted into the PdCI bond and that a nearly linear PdPdSn unit it present infrared and electronic spectral evidence indicates that carbon monoxide and sulfur dioxide insert into the Pd-Pd bond of Pd2(dpm)2(SnCl3)Cl. Spectroscopic evidence for the formation of Pd2(dpm)2(SnCl3)2 is described.

Cryocrystallography : Effect of cooling medium on sample cooling rate

The rates of cooling of small samples with cold N2 gas (100 K), liquid N2 (77 K) and liquid propane (100 K) have been measured. The samples were one bare Cu-constantan thermocouple and one coated with a 0.25 mm layer of silicone rubber cement. Gas cooling yielded the lowest rate, liquid N2 the highest. With the gas, cooling of the centers of the samples from 295 to 140 K took 0.8 and 2 s for the bare and coated samples, respectively; with liquid N2 the times were 0.15 and 0.6 s, and with liquid propane they were 0.15–0.18 and 1.2 s, respectively (time reproducibility is within ±10%).

When VSEPR Fails: Experimental and Theoretical Investigations of the Behavior of Alkaline‐Earth‐Metal Acetylides

The synthesis, structural, and spectral characterization as well as a theoretical study of a family of alkaline-earth-metal acetylides provides insights into synthetic access and the structural and bonding characteristics of this group of highly reactive compounds. Based on our earlier communication that reported unusual geometry for a family of triphenylsilyl-substituted alkaline-earth-metal acetylides, we herein present our studies on an expanded family of target derivatives, providing experimental and theoretical data to offer new insights into the intensively debated theme of structural chemistry in heavy alkaline-earth-metal chemistry.

Atomic Resolution Structure of Concanavalin A at 120 K

The structure of native concanavalin A has been refined to a resolution of 1.2 A against data collected at 120 K. The space group is I222, with a = 61.954 (8), b = 86.053 (11), c = 89.079 (11) A. The structure was refined by restrained weighted least-squares minimization of sum w(F(o)(2) - F(c)(2)(2) with SHELXL92/3/6. The final model contains all of the atoms from 237 amino acids, two metal ions and 271 water molecules spread over 287 sites. Disorder is modelled over two conformations for 30 amino-acid side chains. The final weighted R index on F(2) (wR(2)) on all data was 30.4%. Conventional R indices based on F were 14.2 and 11.8% for all data and for data with F > 4sigma(F), respectively.

Neo-clerodane diterpenoids from Ajuga parviflora

Abstract Three new neo-clerodane diterpenoids, deoxyajugarin-I, ajugarin-I chlorohydrin, and 3β-acetoxy-clerodinin C, have been isolated from Ajuga parviflora collected near Nainital, India. Also isolated were ajugarin-I and II, ajugamarin F4, dihydroclerodin-I, clerodinins C and D and 15-α-ethoxy- and 15-β-ethoxy-14-hydroajugapitin.