New software, OLEX2, has been developed for the determination, visualization and analysis of molecular crystal structures. The software has a portable mouse-driven workflow-oriented and fully comprehensive graphical user interface for structure solution, refinement and report generation, as well as novel tools for structure analysis. OLEX2 seamlessly links all aspects of the structure solution, refinement and publication process and presents them in a single workflow-driven package, with the ultimate goal of producing an application which will be useful to both chemists and crystallographers.

OLEX2: a complete structure solution, refinement and analysis program

J. Appl. Cryst.の発刊に際して

The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal–organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.

https://journals.iucr.org/b/issues/2016/02/00/bm5086/bm5086.pdf

The Cambridge Structural Database

Recent startling interest for lanthanide luminescence is stimulated by the continuously expanding need for luminescent materials meeting the stringent requirements of telecommunication, lighting, electroluminescent devices, (bio-)analytical sensors and bio-imaging set-ups. This critical review describes the latest developments in (i) the sensitization of near-infrared luminescence, (ii) “soft” luminescent materials (liquid crystals, ionic liquids, ionogels), (iii) electroluminescent materials for organic light emitting diodes, with emphasis on white light generation, and (iv) applications in luminescent bio-sensing and bio-imaging based on time-resolved detection and multiphoton excitation (500 references).

/pdf/lanthanide-luminescence-for-functional-materials-and-bio-1w9cppwf8r.pdf

Lanthanide luminescence for functional materials and bio-sciences

The completion of a crystal structure determination is often hampered by the presence of embedded solvent molecules or ions that are seriously disordered. Their contribution to the calculated structure factors in the least-squares refinement of a crystal structure has to be included in some way. Traditionally, an atomistic solvent disorder model is attempted. Such an approach is generally to be preferred, but it does not always lead to a satisfactory result and may even be impossible in cases where channels in the structure are filled with continuous electron density. This paper documents the SQUEEZE method as an alternative means of addressing the solvent disorder issue. It conveniently interfaces with the 2014 version of the least-squares refinement program SHELXL [Sheldrick (2015). Acta Cryst. C71. In the press] and other refinement programs that accept externally provided fixed contributions to the calculated structure factors. The PLATON SQUEEZE tool calculates the solvent contribution to the structure factors by back-Fourier transformation of the electron density found in the solvent-accessible region of a phase-optimized difference electron-density map. The actual least-squares structure refinement is delegated to, for example, SHELXL. The current versions of PLATON SQUEEZE and SHELXL now address several of the unnecessary complications with the earlier implementation of the SQUEEZE procedure that were a necessity because least-squares refinement with the now superseded SHELXL97 program did not allow for the input of fixed externally provided contributions to the structure-factor calculation. It is no longer necessary to subtract the solvent contribution temporarily from the observed intensities to be able to use SHELXL for the least-squares refinement, since that program now accepts the solvent contribution from an external file (.fab file) if the ABIN instruction is used. In addition, many twinned structures containing disordered solvents are now also treatable by SQUEEZE. The details of a SQUEEZE calculation are now automatically included in the CIF archive file, along with the unmerged reflection data. The current implementation of the SQUEEZE procedure is described, and discussed and illustrated with three examples. Two of them are based on the reflection data of published structures and one on synthetic reflection data generated for a published structure.

/pdf/platon-squeeze-a-tool-for-the-calculation-of-the-disordered-2netjer0un.pdf

PLATON SQUEEZE: a tool for the calculation of the disordered solvent contribution to the calculated structure factors

This paper describes the mathematical basis for olex2.refine, the new refinement engine which is integrated within the Olex2 program. Precise and clear equations are provided for every computation performed by this engine, including structure factors and their derivatives, constraints, restraints and twinning; a general overview is also given of the different components of the engine and their relation to each other. A framework for adding multiple general constraints with dependencies on common physical parameters is described. Several new restraints on atomic displacement parameters are also presented.

/pdf/the-anatomy-of-a-comprehensive-constrained-restrained-2bv5vaepqv.pdf

The anatomy of a comprehensive constrained, restrained refinement program for the modern computing environment – Olex2 dissected

D. Intermolecular Ligand Exchange 1996 1. Water Substitution 1996 2. Non-Covalent Binding 1997 V. Excited-State Chemistry 1998 A. Excitation and Quenching 1998 B. Emission Characteristics 1999 C. Responsive Luminescent Systems 2002 VI. Magnetic Resonance Spectroscopy Applications 2004 A. Lanthanide-Induced Shifts (LIS) 2004 B. Applications in Aqueous Media 2005 VII. Acknowledgements 2007 VIII. Supporting Information 2007 IX. References 2007

Being excited by lanthanide coordination complexes: aqua species, chirality, excited-state chemistry, and exchange dynamics.

iotbx.cif is a new software module for the development of applications that make use of the CIF format. Comprehensive tools are provided for input, output and validation of CIFs, as well as for interconversion with high-level cctbx [Grosse-Kunstleve, Sauter, Moriarty & Adams (2002). J. Appl. Cryst. 35, 126–136] crystallographic objects. The interface to the library is written in Python, whilst parsing is carried out using a compiled parser, combining the performance of a compiled language (C++) with the benefits of using an interpreted language.

/pdf/iotbx-cif-a-comprehensive-cif-toolbox-4zyca64sbf.pdf

Horst Puschmann

Papers

OLEX2: a complete structure solution, refinement and analysis program

The anatomy of a comprehensive constrained, restrained refinement program for the modern computing environment – Olex2 dissected

Being excited by lanthanide coordination complexes: aqua species, chirality, excited-state chemistry, and exchange dynamics.

iotbx.cif: a comprehensive CIF toolbox.

The C-glycosylation of flavonoids in cereals.