scholarly journals X-ray crystal structure of endosulfan sulfate

2019 ◽  
Vol 62 (1) ◽  
Author(s):  
Hwa-Kyung Lee ◽  
Jonghwa Lee ◽  
Junghak Lee ◽  
Joon-Kwan Moon ◽  
Jeong-Han Kim
Keyword(s):  
Crystal Structure ◽  
Three Dimensional ◽  
Energy Difference ◽  
Dimensional Structure ◽  
Endosulfan Sulfate ◽  
Chair Form ◽  
X Ray ◽  
X Ray Crystallography ◽  
Total Potential ◽  
Ms Analysis

Abstract X-ray crystallography is an important method used to confirm the three-dimensional structure of a chemical compound. In this study, the crystal structure of endosulfan sulfate was investigated. Endosulfan sulfate is the major metabolite of the insecticide endosulfan, which is composed of two stereoisomers (α and β). From GC–MS analysis, α- and β-endosulfan each gave a single peak in the endosulfan sample, but only one peak was observed for endosulfan sulfate. Interestingly, in X-ray crystallography, two conformers of endosulfan sulfate (A and B) were observed at a ratio of 2(A):1(B). A heterocyclic seven-membered ring of conformer B assumed a horizontal-chair form, differing from two twisted forms of α-endosulfan while a vertical-chair form was observed for conformer A, showing the very similar structure to β-endosulfan; this difference in conformation is caused by differing bond angles at O(1)–C(8)–C(3) and O(2)–C(9)–C(4). In space packing, two asymmetric units were obtained, and three molecules were aligned in the order of A–A–B conformers in each unit. The total potential energy of A was slightly lower (approximately 4 kcal/mol) than B, possibly resulting in the two molecules of A that exist in a rigid crystal state. However, A and B conformers should not exist at room temperature in a solution state for GC–MS analysis, likely due to the small energy difference.

scholarly journals An Unexpected Trinuclear Cobalt(II) Complex Based on a Half-Salamo-Like Ligand: Synthesis, Crystal Structure, Hirshfeld Surface Analysis, Antimicrobial and Fluorescent Properties

Crystals ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 408 ◽  
Author(s):  
Ruo-Yan Li ◽  
Xiao-Xin An ◽  
Juan-Li Wu ◽  
You-Peng Zhang ◽  
Wen-Kui Dong
Keyword(s):  
Crystal Structure ◽  
Surface Analysis ◽  
Three Dimensional ◽  
Antimicrobial Activities ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
Fluorescent Properties ◽  
X Ray ◽  
X Ray Crystallography ◽  
Elemental Analyses

An unexpected trinuclear Co(II) complex, [Co3(L2)2(μ-OAc)2(CH3OH)2]·2CH3OH (H2L2 = 4,4′-dibromo-2,2′-[ethylenedioxybis(nitrilomethylidyne)]diphenol) constructed from a half-Salamo-based ligand (HL1 = 2-[O-(1-ethyloxyamide)]oxime-4-bromophenol) and Co(OAc)2·4H2O, has been synthesized and characterized by elemental analyses, infrared spectra (IR), UV-Vis spectra, X-ray crystallography and Hirshfeld surface analysis. The Co(II) complex contains three Co(II) atoms, two completely deprotonated (L2)2− units, two bridged acetate molecules, two coordinated methanol molecules and two crystalline methanol molecules, and finally, a three-dimensional supramolecular structure with infinite extension was formed. Interestingly, during the formation of the Co(II) complex, the ligand changed from half-Salamo-like to a symmetrical single Salamo-like ligand due to the bonding interactions of the molecules. In addition, the antimicrobial activities of HL1 and its Co(II) complex were also investigated.

scholarly journals Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

2018 ◽  
Vol 19 (11) ◽  
pp. 3401 ◽  
Author(s):  
Ashutosh Srivastava ◽  
Tetsuro Nagai ◽  
Arpita Srivastava ◽  
Osamu Miyashita ◽  
Florence Tama
Keyword(s):  
Protein Dynamics ◽  
Computational Methods ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Insight Into

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

scholarly journals Topography Prediction of Helical Transmembrane Proteins by a New Modification of the Sliding Window Method

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Maria N. Simakova ◽  
Nikolai N. Simakov
Keyword(s):  
Membrane Proteins ◽  
Transmembrane Domain ◽  
Domain Boundary ◽  
Three Dimensional ◽  
Transmembrane Proteins ◽  
Sliding Window ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Window Method

Protein functions are specified by its three-dimensional structure, which is usually obtained by X-ray crystallography. Due to difficulty of handling membrane proteins experimentally to date the structure has only been determined for a very limited part of membrane proteins (<4%). Nevertheless, investigation of structure and functions of membrane proteins is important for medicine and pharmacology and, therefore, is of significant interest. Methods of computer modeling based on the data on the primary protein structure or the symbolic amino acid sequence have become an actual alternative to the experimental method of X-ray crystallography for investigating the structure of membrane proteins. Here we presented the results of the study of 35 transmembrane proteins, mainly GPCRs, using the novel method of cascade averaging of hydrophobicity function within the limits of a sliding window. The proposed method allowed revealing 139 transmembrane domains out of 140 (or 99.3%) identified by other methods. Also 236 transmembrane domain boundary positions out of 280 (or 84%) were predicted correctly by the proposed method with deviation from the predictions made by other methods that does not exceed the detection error of this method.

New Inclusion Compounds of Selenourea with Tetraethyl- and Tetra-n-propylammonium Halides

1997 ◽  
Vol 53 (2) ◽  
pp. 262-271 ◽  
Author(s):  
Q. Li ◽  
T. C. W. Mak
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Crystal Data ◽  
Tetraethylammonium Chloride ◽  
Space Group ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dimensional Network ◽  
Single Column

Air-sensitive selenourea inclusion complexes tetraethylammonium chloride–selenourea (1/2), (C2H5)4N+.C1−.2[(NH2)2CSe] (1), tetra-n-propyl-ammonium chloride–selenourea (1/3), (n-C3H7)4N+.C1−.3[(NH2)2CSe] (2), tetra-n-propylammonium bromide–selenourea (1/3), (n-C3H7)4N+.Br−.3[(NH2)2CSe] (3), and tetra-n-propylammonium iodide–selenourea (1/1), (n-C3H7)4N+.I−.(NH2)2CSe (4), have been prepared and characterized by X-ray crystallography. Crystal data, Mo Kα radiation: (1), space group P21/n, Z = 4, a = 8.768 (5), b = 11.036 (6), c = 19.79 (1) Å, β = 96.92 (1)°, R F = 0.055 for 1468 observed data; (2), space group Cc, Z = 4, a = 18.091 (4), b = 13.719 (3), c = 11.539 (2) Å, β = 111.93 (3)°, R F = 0.051 for 1187 observed data; (3), space group Cc, Z = 4, a = 18.309  (4), b = 13.807 (3), c = 11.577 (2) Å, β = 112.45 (3)°, R F = 0.049 for 1592 observed data; (4), space group P21/n, Z = 4, a = 8.976 (1), b = 14.455 (2), c = 15.377 (3) Å, β = 94.16(1)°, R F = 0.062 for 1984 observed data. In the crystal structure of (1) the parallel alternate arrangement of selenourea–chloride ribbons and selenourea chains generates a puckered layer and the cations are sandwiched between them. In the isomorphous complexes (2) and (3) wide selenourea–halide double ribbons are crosslinked by bridging selenourea molecules via N—H...Se and N—H...X hydrogen bonds [average N...Se = 3.521 (8) and 3.527 (7), N...Cl = 3.354 (8) and N...Br = 3.500 (7) Å in (2) and (3), respectively] to form a channel-like three-dimensional network and the cations are accommodated in a single column within each channel. In the crystal structure of (4) the selenourea molecules are joined in the shoulder-to-shoulder fashion via N—H...Se hydrogen bonds [N...Se = 3.529 (7) and 3.534 (7) Å] to generate a ribbon and each selenourea molecule also forms a pair of chelating N—H...I hydrogen bonds [N...I = 3.567 (7) and 3.652 (7) Å] to an adjacent iodide ion.

scholarly journals A new on-axis multimode spectrometer for the macromolecular crystallography beamlines of the Swiss Light Source

2009 ◽  
Vol 16 (2) ◽  
pp. 173-182 ◽  
Author(s):  
Robin L. Owen ◽  
Arwen R. Pearson ◽  
Alke Meents ◽  
Pirmin Boehler ◽  
Vincent Thominet ◽  
...  
Keyword(s):  
Light Source ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Additional Information ◽  
Swiss Light Source ◽  
Induced Changes ◽  
Insight Into

X-ray crystallography at third-generation synchrotron sources permits tremendous insight into the three-dimensional structure of macromolecules. Additional information is, however, often required to aid the transition from structure to function. In situ spectroscopic methods such as UV–Vis absorption and (resonance) Raman can provide this, and can also provide a means of detecting X-ray-induced changes. Here, preliminary results are introduced from an on-axis UV–Vis absorption and Raman multimode spectrometer currently being integrated into the beamline environment at X10SA of the Swiss Light Source. The continuing development of the spectrometer is also outlined.

scholarly journals Induction of Rare Conformation of Oligosaccharide by Binding to Calcium-dependent Bacterial Lectin: X-ray Crystallography and Modelling Study

2019 ◽  
Author(s):  
Martin Lepsik ◽  
Roman Sommer ◽  
Sakonwan Kuhaudomlarp ◽  
Mickaёl Lelimousin ◽  
Emanuele Paci ◽  
...  
Keyword(s):  
Force Field ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Lewis X ◽  
X Ray ◽  
X Ray Crystallography ◽  
Calcium Dependent ◽  
Protein Receptors ◽  
Dependent Protein ◽  
Micro Organisms

ABSTRACTPathogenic micro-organisms utilize protein receptors in adhesion to host tissues, a process that in some cases relies on the interaction between lectin and human glycoconjugates. Oligosaccharide epitopes are recognized through their three-dimensional structure and their flexibility is a key issue in specificity. In this paper, we analyse by X-ray crystallography the structures of the lectin LecB from two strains of Pseudomonas aeruginosa in complex with Lewis x oligosaccharide present on cell surfaces of human tissues. An unusual conformation of the glycan was observed in all binding sites with a non-canonical syn orientation of the N-acetyl group of N-acetyl-glucosamine. A PDB-wide search revealed that such an orientation occurs only in 2% of protein/carbohydrate complexes. Theoretical chemistry calculations showed that the observed conformation is unstable in solution but stabilised by the lectin. A reliable description of LecB/Lewis x complex by force field-based methods had proven as especially challenging due to the special feature of the binding site, two closely apposed Ca2+ ions which induce strong charge delocalisation. By comparing various force-field parametrisations, we design general protocols which will be useful in near future for designing carbohydrate-based ligands (glycodrugs) against other calcium-dependent protein receptors.

Synopses from the poster exhibition organized by I. M. Kerr, 1. Interferon: a tertiary structure predicted from amino acid sequences

1982 ◽  
Vol 299 (1094) ◽  
pp. 125-127 ◽  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
X Ray ◽  
Three Dimensional Structure ◽  
X Ray Crystallography ◽  
Functional Studies

Functional studies on interferon would be helped by a three-dimensional structure for the molecule. However, it may be several years before the structure of the protein is determined by X-ray crystallography. We have therefore used available methods for predicting the secondary - and the tertiary - structure of a protein from its amino acid sequence to propose a tertiary model involving the packing of four a-helices. Details of this work have been published elsewhere (Sternberg & Cohen 1982).

scholarly journals Crystal structure of a 1:1 salt of 4-aminobenzoic acid (vitamin B10) with pyrazinoic acid

2018 ◽  
Vol 74 (12) ◽  
pp. 1923-1927 ◽  
Author(s):  
K. V. Drozd ◽  
S. G. Arkhipov ◽  
E. V. Boldyreva ◽  
G. L. Perlovich
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Aminobenzoic Acid ◽  
X Ray Diffraction ◽  
Title 1 ◽  
X Ray ◽  
Pyrazinoic Acid ◽  
And Calorimetry

The title 1:1 salt, C7H8NO2+·C5H3N2O2−(systematic name: 4-carboxyanilinium pyrazine-2-carboxylate), was synthesized successfully by slow evaporation of a saturated solution from water–ethanol (1:1v/v) mixture and characterized by X-ray diffraction (SCXRD, PXRD) and calorimetry (DSC). The crystal structure of the salt was solved and refined at 150 and 293 K. The salt crystallizes with one molecule of 4-aminobenzoic acid (PABA) and one molecule of pyrazinoic acid (POA) in the asymmetric unit. In the crystal, the PABA and POA molecules are associated via COOH...Naromheterosynthons, which are connected by N—H...O hydrogen bonds, creating zigzag chains. The chains are further linked by N—H...O hydrogen bonds and π–π stacking interactions along thebaxis [centroid-to-centroid distances = 3.7377 (13) and 3.8034 (13) Å at 150 and 293 K, respectively] to form a layered three-dimensional structure.

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