[16] SHELXL: High-resolution refinement
Publisher Summary
SHELXL-93 was originally written as a replacement for the refinement part of the small-molecule program SHELX-76. The program is designed to be easy to use and general for all space groups and uses a conventional structure-factor calculation rather than a fast Fourier transform (FFT) summation. The latter would be faster but in practice involves some small approximations and is not suitable for the treatment of anomalous dispersion or anisotropic thermal motion. The price to pay for the extra precision and generality is that SHELXL is much slower than programs written specifically for macromolecules. This is compensated for, to some extent, by the better convergence properties, reducing the amount of manual intervention required. A new version, SHELXL-97, was released in May 1997; this is the version described in the chapter. The changes are primarily designed to make the program easier to use for macromolecules. Advances in cryogenic techniques, area detectors, and the use of synchrotron radiation enable macromolecular data to be collected to higher resolution than was previously possible. In practice, this tends to complicate the refinement because it is possible to resolve finer details of the structure. It is often necessary to model alternative conformations, and in a few cases, even anisotropic refinement is justified.
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Cited by (1924)
Hyperatins A–D, highly oxidized polycyclic polyprenylated acylphloroglucinols from Hypericum perforatum L. with hypoglycemic potential in liver cells
2024, PhytochemistryHyperatins A–D (1–4), four previously undescribed polycyclic polyprenylated acylphloroglucinols, were isolated from Hypericum perforatum L. (St. John's wort). Compound 1 possessed a unique octahydroindeno[1,7a-b]oxirene ring system with a rare 2,7-dioxabicyclo[2.2.1]heptane fragment. Compounds 2–4 had an uncommon decahydrospiro[furan-3,7′-indeno[7,1-bc]furan] ring system. Their structures were established by spectroscopic analyses and X-ray crystallography. Plausible biosynthetic pathways of 1–4 were also proposed. Compounds 1 and 2 exerted promising hypoglycemic activity by inhibiting glycogen synthase kinase 3 expression in liver cells.
Theoretical and experimental cocrystal screening of temozolomide with a series of phenolic acids, promising cocrystal coformers
2024, Chinese Chemical LettersThe virtual cocrystal screening approach based on molecular electrostatic potential surface (MEPS) maps is a fast and feasible computational method to estimate the probability of cocrystal formation by calculating the difference in the interaction site pairing energies of monomers and that of their assemblies prior to experimental screening. In this paper, we report 12 cocrystal forms of temozolomide with mono-, di-, and trihydroxy benzoic acids, namely, 3‑hydroxy-, 2,4-dihydroxy-, 2,5-dihydroxy-, 2,6-dihydroxy-, 3,4-dihydroxy-, and 3,4,5-trihydroxy-benzoic acids, as well as benzoic acid, as pharmaceutical coformers for the first time. 10 single crystals out of the 12 cocrystal forms were obtained and unequivocally determined by single-crystal X-ray diffraction, which clarified spatial arrangements, molecular conformations, and supramolecular synthons. MEPS further gains some insights into the sites of hydrogen bonding interactions for exploring combination patterns in these assemblies. Modulated stability of TMZ was successfully achieved by cocrystallization with these acids.
Structural consequences in differently substituted haloarylcarboxylates and non-covalent interactions on crystal packing and biological efficacy of copper(II) complexes with N,N,N′,N′-tetramethylethylenediamine N-donor ligand
2024, Journal of Molecular StructureIn this work, we reported four new copper(II) halo-benzoate complexes (2-chloro-4-nitrobenzoate (2-Cl-4-NO2-BZ), 3,5-DICBZ, 2-chloro-5-nitrobenzoate (2-Cl-5-NO2-BZ), 3,5-difluoro benzoate (3,5-DIFBZ), and 3,5-dichlorobenzene (3,5-DICBZ) respectively in complexes 1–4) with N,N,N’,N’- tetramethylethylene diamine (temed) N-donor ligand in order to study the interesting coordination features and biological evaluation of such complexes under ambient reaction conditions. All the complexes 1–4 were characterized by elemental analyses, and spectroscopic techniques, including FT-IR, UV–vis, and EPR etc. Single crystal X-ray structure determination (SCXRD) of complexes revealed the distorted octahedral geometry in all complexes. Notably, the halobenzoate ligands exhibited a bidentate chelation mode in complexes 1 and 2, while they showed a monodentate mode in complex 3. In complex 4, the carboxylate ligand exhibited both monodentate as well as bidentate coordination. Furthermore, detailed packing analyses of complexes 1–4 highlighted the significance of halogen bonding in lattice stabilization besides hydrogen bonding and π∙∙∙π interactions as evidenced by Hirshfeld surface analyses and crystal analysis. Moreover, packing analyses displayed that complex 1 exhibited a layered or wave-like arrangement, while complex 2 featured a helical arrangement supported by a supramolecular halogen-bonded network guided by Cl∙∙∙O interactions. Complex 3 displayed a zig-zag layered arrangement with a stacking topology, and Complex 4 showcased a ribbon-like arrangement stabilized by F∙∙∙F and Cl∙∙∙Cl halogen bonding interactions. Furthermore, sigma hole on halogen atoms has also been examined (which play an important role in halogen bonding) by electrostatic-potential isosurfaces. In order to exploit the biological efficacy of complexes 1–4 owing to the inherent biological activity of copper metal, molecular docking analyses against gram +ve bacteria i.e. S. epidermidis (PDB ID; 8DO6), B. subtilis (1QD9), as well as two gram -ve bacteria, namely, P. aeruginosa (5WZE) and S. dysenteriae (1DM0), have also been carried out. Interestingly, values of docking scores and inhibition constant of all complexes 1–4 (with a maximum binding score (inhibition constant) of -9.8 kcal/mol (0.063 µMol) in 1 against 8DO6 and 1DM0) revealed higher biological efficacy than that of standard drugs.
Subatomic structure of orthorhombic thaumatin at 0.89 Å reveals that highly flexible conformations are crucial for thaumatin sweetness
2024, Biochemical and Biophysical Research CommunicationsThaumatin is a sweet-tasting protein that elicits a sweet taste at a threshold of approximately 50 nM. Structure-sweetness relationships in thaumatin suggest that the basicity of two amino acids residues, Arg82 and Lys67, are particularly responsible for sweetness. Using tetragonal crystals, our structural analysis suggested that flexible sidechain conformations of these two residues play an important role in sweetness. However, in tetragonal crystals, Arg82 is adjacent to symmetry-related residues, and its flexibility is relatively restrained by the crystal packing. To reduce and diminish these symmetry-related effects, orthorhombic crystals were prepared, and their structures were successfully determined at a resolution of 0.89 Å. Within the orthorhombic lattice, two alternative conformations were more clearly visible at Lys67 than in a tetragonal system. Interestingly, for the first time, three alternative conformations at Arg82 were only found in an orthorhombic system. These results suggest the importance of flexible conformations in sweetness determinants. Such subtle structural variations might serve to adjust the complementarity of the electrostatic potentials of sweet receptors, thereby eliciting the potent sweet taste of thaumatin.
New nitrogen-containing lanthanide complexes with novel structural, thermal, and fluorescence properties
2024, Journal of Saudi Chemical SocietyFive new lanthanide complexes were synthesized using 5,5′ -dimethyl-2,2′ bipyridine(5,5′-DM-2,2′-bipy) and 3-Dimethylaminobenzoic acid(3-N,N-DMHBA) as ligands, and all five lanthanide complexes were found to be dimeric by single crystal X-ray diffraction. The general chemical formula is [Ln(3-N,N-DMBA)3(5,5′-DM-2,2′-bipy)]2·2(3-N,N-DMHBA), Ln=(La(1), Pr(2), Dy(3), Eu(4)), [Ln(3-N,N-DMBA)3(5,5′-DM-2,2′-bipy)]2, Ln=(Sm(5)). 3-N,N-DMBA = 3-Dimethylaminobenzoate. DTG-DSC/FTIR coupling technique was used to examine the thermal decomposition mechanism of the five lanthanide complexes, and the fluorescence properties of complexes 3, 4 and 5 were also measured. The fluorescence lifetime of complex 4 was 0.6941(3) ms. The mono- and trimorphic states of the ligand were calculated by DFT. The mechanism of luminescence of the complexes was explained from the point of view of energy transfer.
Synthesis, crystal structure, and intrinsic reactivity descriptors of coordination complexes of [(cis-PdCl<inf>2</inf>·L-proline) L-proline] and [trans-PdCl<inf>2</inf>·(glycine-OMe)<inf>2</inf>]
2023, Journal of Molecular StructureThis work describes the synthesis and structural characterization of two palladium (II) complexes elucidated by infrared spectroscopy, dispersive energy analysis (EDS) with Scanning Electron Microscopy (SEM) and X-ray single-crystal diffraction analysis. The first chiral complex is derivatized from l-proline amino acid, obtaining [Cis-PdCl2·L-proline(L-proline)] (1), in which the structure does not have symmetry elements and crystallized in a triclinic crystal system on a non-centrosymmetric space group P1. The comparison with the structural complex of [trans-PdCl2·(glycine-OMe)2] (3) becomes necessary due to the anticancer activity of its analog, cis-platinum, and the catalytic activity caused by Pd as a metallic center. Complex 1 is therefore made up of a free proline molecule linked by a single hydrogen bond to a PdCl2 molecule forming a 5-member chelate ring of the COO···Pd···NH type with another proline molecule and displaying distorted angles and bond sizes to the square planar geometry of the palladium (Pd) center. Ring formation generates a new stereogenic center chemically correlated with the induction caused by the absolute configuration S of the initial amino acid. The crystal results strongly indicate the confirmed configuration by the Flack parameter and its crystal packing stabilization by an intermolecular H-bond network, highlighting as a secondary mimicking structure the β sheets formed by hydrogen bonding interaction of the N—H···Cl type responsible for the disorder moldered on pyrrolidine ring.
Furthermore, the Pd(II) complex obtained by the glycine was [trans-PdCl2·(glycine-OMe)2] (3). Regarding its chemical structure, this complex is constituted by the union of two glycine methyl ester molecules binding to a Pd in a trans disposition concerning the almost perfect square plane, which also contains a C2 axis of rotation. Complex 3 crystallized in a monoclinic system and centrosymmetric space group P21/c, the packing is favored by four strong hydrogen bond type interactions presenting helices with 90° rotations between each layer.
Owing to their great interest and relevance in Pd—N amino acid in catalytic and medicinal chemistry, the electronic and global reactivity properties of complexes 1 and 3 were further explored by computational methods in the framework of Density Functional Theory, finding 1 as the most reactive complex due to the narrower E-LUMO/E-HOMO energy gap, having this band gap in agreement with the lowest hardness value compared to those shown for 3, in which band gap and hardness are higher with a tendency to kinetic stability and controlled reactivity.