Search results for "structure determination"
showing 9 items of 19 documents
Inverse simulated annealing: Improvements and application to amorphous InSb
2014
An improved inverse simulated annealing method is presented to determine the structure of complex disordered systems from first principles in agreement with available experimental data or desired predetermined target properties. The effectiveness of this method is demonstrated by revisiting the structure of amorphous InSb. The resulting network is mostly tetrahedral and in excellent agreement with available experimental data.
Structural Characterization of Organics Using Manual and Automated Electron Diffraction
2010
In the last decade the importance of transmission electron microscopic studies has become increasingly important with respect to the characterization of organic materials, ranging from small organic molecules to polymers and biological macromolecules. This review will focus on the use of transmission electron microscope to perform electron crystallography experiments, detailing the approaches in acquiring electron crystallographic data. The traditional selected area approach and the recently developed method of automated diffraction tomography (ADT) will be discussed with special attention paid to the handling of electron beam sensitive organic materials.
The Protein Structure Context of PolyQ Regions.
2016
Proteins containing glutamine repeats (polyQ) are known to be structurally unstable. Abnormal expansion of polyQ in some proteins exceeding a certain threshold leads to neurodegenerative disease, a symptom of which are protein aggregates. This has led to extensive research of the structure of polyQ stretches. However, the accumulation of contradictory results suggests that protein context might be of importance. Here we aimed to evaluate the structural context of polyQ regions in proteins by analysing the secondary structure of polyQ proteins and their homologs. The results revealed that the secondary structure in polyQ vicinity is predominantly random coil or helix. Importantly, the region…
The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013
2015
The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could…
Analysis of the structural quality of the CASD-NMR 2013 entries.
2015
We performed a comprehensive structure validation of both automated and manually generated structures of the 10 targets of the CASD-NMR-2013 effort. We established that automated structure determination protocols are capable of reliably producing structures of comparable accuracy and quality to those generated by a skilled researcher, at least for small, single domain proteins such as the ten targets tested. The most robust results appear to be obtained when NOESY peak lists are used either as the primary input data or to augment chemical shift data without the need to manually filter such lists. A detailed analysis of the long-range NOE restraints generated by the different programs from t…
Synthesis, crystal and molecular-electronic structure, and kinetic investigation of two new sterically hindered isomeric forms of the dimethyl[methyl…
2017
Two new structural isomers – 2,4-dimethyl-5-[methyl(phenylsulfonyl)amino]benzenesulfonyl chloride (1) and 2,4-dimethyl-3-[methyl(phenylsulfonyl)amino]benzenesulfonyl chloride (2) were synthesized by interaction of N-(2,4-dimethylphenyl)-N-methyl-benzenesulfonamide or N-(2,6-dimethylphenyl)-N-methylbenzenesulfonamide with chlorosulfonic acid. Both compounds have been structurally characterized by X-ray single crystal diffraction at 100 K. The crystals of 1 are triclinic: space group View the MathML source, a = 8.1542(2), b = 11.0728(3), c = 11.2680(3) Å, α = 116.557(3), β = 95.155(2), γ = 108.258(2)°, V = 831.97(4) Å3, Z = 2, R = 0.0251 for 2429 reflections; the crystals of 2 are monoclinic:…
π-Electron delocalization in 2-benzoyl-5-phenylpyrazolidin-3-one
2018
Abstract The crystal and molecular structures of 2-benzoyl-5-phenylpyrazolidin-3-one have been characterized by X-ray diffraction along with density functional theory studies. Cinnamic acid chloride was reacted with benzhydrazide, yielding 2-benzoyl-5-phenylpyrazolidin-3-one. This product was formed in the transformation comprising the nucleophilic addition of benzhydrazide to the styryl fragment of the α,β-unsaturated arrangement and subsequent cyclization. The molecule contains two benzene rings and one five-membered heterocyclic ring with an N–N single bond. The five-membered ring is composed of three atoms of sp 3 hybridization and two atoms of sp 2 hybridization, which cause the flatte…
Triclinic conformational polymorph of N,N,N′,N′-tetrakis(2-cyanoethyl)-1,2-ethylenediamine (TCED)
2018
Abstract The crystal and molecular structures of two polymorphs of N,N,N′,N′-tetrakis(2-cyanoethyl)-1,2-ethylenediamine have been characterized by X-ray diffraction along with density functional theory (DFT) studies. The molecules differ from each other by conformation. N,N,N′,N′-tetrakis(2-cyanoethyl)-1,2-ethylenediamine has been synthesized by cyanoethylation of ethylenediamine. Cyanoethylation of vicinal diamines is important for the synthesis of hyperbranched polymeric materials applied as catalysts, surfactants and encapsulating agents in drug delivery systems. The molecular geometry of N,N,N′,N′-tetracyanoethyl-1,2-ethylenediamine is similar to that of homologous compounds. DFT calcul…
Structural insights into M2O-Al2O3-WO3 (M = Na, K) system by electron diffraction tomography.
2015
TheM2O–Al2O3–WO3(M= alkaline metals) system has attracted the attention of the scientific community because some of its members showed potential applications as single crystalline media for tunable solid-state lasers. These materials behave as promising laser host materials due to their high and continuous transparency in the wide range of the near-IR region. A systematic investigation of these phases is nonetheless hampered because it is impossible to produce large crystals and only in a few cases a pure synthetic product can be achieved. Despite substantial advances in X-ray powder diffraction methods, structure investigation on nanoscale is still challenging, especially when the sample i…