ORTEP-3 for Windows - a version of ORTEP-III with a Graphical User Interface (GUI)

Abstract: The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and signi®cant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should follow the standard format given on page 189 of the June 1985 issue of the Journal [J. Appl. Cryst. (1985). 18, 189± 190] and on the World Wide Web at http://www.iucr. org/journals/jac/software/. Lists of software presented and/or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known.

Abstract: The WinGX suite provides a complete set of programs for the treatment of small-molecule single-crystal diffraction data, from data reduction and processing, structure solution, model refinement and visualization, and metric analysis of molecular geometry and crystal packing, to final report preparation in the form of a CIF. It includes several well known pieces of software and provides a repository for programs when the original authors no longer wish to, or are unable to, maintain them. It also provides menu items to execute external software, such as the SIR and SHELX suites of programs. The program ORTEP for Windows provides a graphical user interface (GUI) for the classic ORTEP program, which is the original software for the illustration of anisotropic displacement ellipsoids. The GUI code provides input capabilities for a wide variety of file formats, and extra functionality such as geometry calculations and ray-traced outputs. The programs WinGX and ORTEP for Windows have been distributed over the internet for about 15 years, and this article describes some of the more modern features of the programs.

Abstract: The structure at 100 K of integral membrane light-harvesting complex II (LH2) from Rhodopseudomonas acidophila strain 10050 has been refined to 2.0 A resolution. The electron density has been significantly improved, compared to the 2.5 A resolution map, by high resolution data, cryo-cooling and translation, libration, screw (TLS) refinement. The electron density reveals a second carotenoid molecule, the last five C-terminal residues of the α-chain and a carboxy modified α-Met1 which forms the ligand of the B800 bacteriochlorophyll. TLS refinement has enabled the characterisation of displacements between molecules in the complex. B850 bacteriochlorophyll molecules are arranged in a ring of 18 pigments composed of nine approximate dimers. These pigments are strongly coupled and at their equilibrium positions the excited state dipole interaction energies, within and between dimers, are ∼370 cm−1 and 280 cm−1, respectively. This difference in coupling energy is similar in magnitude to changes in interaction energies arising from the pigment displacements described by TLS tensors. The displacements appear to be non-random in nature and appear to be designed to optimise the modulation of pigment energy interactions. This is the first time that LH2 pigment displacements have been quantified experimentally. The calculated energy changes indicate that there may be significant contributions to inter-pigment energy interactions from molecular displacements and these may be of importance to photosynthetic energy transfer.

Abstract: A series of relatively low-cost ionic liquids, based on the N-butyronitrile pyridinium cation [C(3)CNpy](+), designed to improve catalyst retention, have been prepared and evaluated in Suzuki and Stille coupling reactions. Depending on the nature of the anion, these salts react with palladium chloride to form [C(3)CNpy](2)[PdCl(4)] when the anion is Cl(-) and complexes of the formula [PdCl(2)(C(3)CNpy)(2)][anion](2) when the anion is PF(6)(-), BF(4)(-), or N(SO(2)CF(3))(2)(-). The solid-state structures of [C(3)CNpy]Cl and [C(3)CNpy](2)[PdCl(4)] have been established by single-crystal X-ray diffraction. The catalytic activity of these palladium complexes following immobilization in both N-butylpyridinium and nitrile-functionalized ionic liquids has been evaluated in Suzuki and Stille coupling reactions. All of the palladium complexes show good catalytic activity, but recycling and reuse is considerably superior in the nitrile-functionalized ionic liquid. Inductive coupled plasma spectroscopy reveals that the presence of the coordinating nitrile moiety in the ionic liquid leads to a significant decrease in palladium leaching relative to simple N-alkylpyridinium ionic liquids. Palladium nanoparticles have been identified as the active catalyst in the Stille reaction and were characterized using transmission electron microscopy.