Jan Rohlíček

Bio: Jan Rohlíček is an academic researcher from Academy of Sciences of the Czech Republic. The author has contributed to research in topics: Crystal structure & Powder diffraction. The author has an hindex of 14, co-authored 73 publications receiving 631 citations. Previous affiliations of Jan Rohlíček include Institute of Chemical Technology in Prague.

MCE2005– a new version of a program for fast interactive visualization of electron and similar density maps optimized for small molecules

Abstract: A new version of MCE is described. This new version supports atom-position generation based on space groups and can display more unit cells around the basic unit cell. The display settings have been improved to allow the colors of the background, atoms and maps to be changed.

Antiferrodistortive phase transition in EuTiO3

Abstract: X-ray diffraction, dynamical mechanical analysis, and infrared reflectivity studies revealed an antiferrodistortive phase transition in EuTiO${}_{3}$ ceramics. Near 300 K, the perovskite structure changes from cubic $Pm\overline{3}m$ to tetragonal $I4/mcm$ due to antiphase tilting of oxygen octahedra along the $\mathbf{c}$ axis (${a}^{0}{a}^{0}{c}^{\ensuremath{-}}$ in Glazer notation). The phase transition is analogous to SrTiO${}_{3}$. However, some ceramics as well as single crystals of EuTiO${}_{3}$ show different infrared reflectivity spectra bringing evidence of a different crystal structure. In such samples, electron diffraction revealed an incommensurate tetragonal structure with modulation wave vector q $\ensuremath{\simeq}$ 0.38 a${}^{*}$. Extra phonons in samples with modulated structure are activated in the IR spectra due to folding of the Brillouin zone. We propose that defects such as Eu${}^{3+}$ and oxygen vacancies strongly influence the temperature of the phase transition to antiferrodistortive phase as well as the tendency to incommensurate modulation in EuTiO${}_{3}$.

CrystalCMP: an easy‐to‐use tool for fast comparison of molecular packing

Abstract: A new approach is introduced for the comparison of molecular packing and the identification of identical crystal structure motifs. It has been tested on data sets for the solid forms of benzamide, cabergoline and trospium. In this approach, the packing similarity is calculated using a simple formula involving the distances between molecular centres and the relative orientations of molecular entities inside a finite molecular cluster. The approach is independent of the atomic labelling, the unit-cell parameters, the space group setting and the number of molecules in the asymmetric part of the unit cell. Owing to its low sensitivity to volume changes, this approach allows the comparison of various solid forms (such as polymorphs, hydrates, solvates, co-crystals or salts) of identical or similar molecular compounds. The method is also suitable for identifying similar results from direct space methods, which are often used in powder diffraction.

Phosphinic Acid Based Linkers: Building Blocks in Metal-Organic Framework Chemistry.

Abstract: Metal-organic frameworks (MOFs) are a chemically and topologically diverse family of materials composed of inorganic nodes and organic linkers bound together by coordination bonds. Presented here are two significant innovations in this field. The first is the use of a new coordination group, phenylene-1,4-bis(methylphosphinic acid) (PBPA), a phosphinic acid analogue of the commonly used terephtalic acid. Use of this new linker group leads to the formation of a hydrothermally stable and permanently porous MOF structure. The second innovation is the application of electron-diffraction tomography, coupled with dynamic refinement of the EDT data, to the elucidation of the structure of the new material, including the localization of hydrogen atoms.

Crystallographic Computing System JANA2006: General features

Abstract: Abstract JANA2006 is a freely available program for structure determination of standard, modulated and magnetic samples based on X-ray or neutron single crystal/ powder diffraction or on electron diffraction. The system has been developed for 30 years from specialized tool for refinement of modulated structures to a universal program covering standard as well as advanced crystallography. The aim of this article is to describe the basic features of JANA2006 and explain its scope and philosophy. It will also serve as a basis for future publications detailing tools and methods of JANA.

CRYSTALS enhancements: dealing with hydrogen atoms in refinement

Abstract: Because they scatter X-rays weakly, H atoms are often abused or neglected during structure refinement. The reasons why the H atoms should be included in the refinement and some of the consequences of mistreatment are discussed along with selected real examples demonstrating some of the features for hydrogen treatment that can be found in the software suite CRYSTALS.

3D Electron Diffraction: The Nanocrystallography Revolution.

Abstract: Crystallography of nanocrystalline materials has witnessed a true revolution in the past 10 years, thanks to the introduction of protocols for 3D acquisition and analysis of electron diffraction data. This method provides single-crystal data of structure solution and refinement quality, allowing the atomic structure determination of those materials that remained hitherto unknown because of their limited crystallinity. Several experimental protocols exist, which share the common idea of sampling a sequence of diffraction patterns while the crystal is tilted around a noncrystallographic axis, namely, the goniometer axis of the transmission electron microscope sample stage. This Outlook reviews most important 3D electron diffraction applications for different kinds of samples and problematics, related with both materials and life sciences. Structure refinement including dynamical scattering is also briefly discussed.