Silver(I) coordination polymers assembled from flexible cyclotriphosphazene ligand: structures, topologies and investigation of the counteranion effects

2016 ◽  
Vol 72 (3) ◽  
pp. 344-356 ◽  
Author(s):  
Derya Davarcı ◽  
Rüştü Gür ◽  
Serap Beşli ◽  
Elif Şenkuytu ◽  
Yunus Zorlu
Keyword(s):  
Coordination Polymers ◽  
Layered Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Two Dimensional ◽  
X Ray ◽  
X Ray Crystallography ◽  
Different Types ◽  
Argentophilic Interactions ◽  
Point Symbol

The reactions of a flexible ligand hexakis(3-pyridyloxy)cyclotriphosphazene (HPCP) with a variety of silver(I) salts (AgX;X= NO3−, PF6−, ClO4−, CH3PhSO3−, BF4−and CF3SO3−) afforded six silver(I) coordination polymers, namely {[Ag2(HPCP)]·(NO3)2·H2O}n(1), {[Ag2(HPCP)(CH3CN)]·(PF6)2}n(2), {[Ag2(HPCP)(CH3CN)]·(ClO4)2}n(3), [Ag3(HPCP)(CH3PhSO3)3]n(4), [Ag2(HPCP)(CH3CN)(BF4)2]n(5) and {[Ag(HPCP)]·(CF3SO3)}n(6). All of the isolated crystalline compounds were structurally determined by X-ray crystallography. Changing the counteranions in the reactions, which were conducted under similar conditions ofM/Lratio (1:1), temperature and solvent, resulted in structures with different types of topologies. In complexes (1)–(6), the ligand HPCP shows different coordination modes with AgIions giving two-dimensional layered structures and three-dimensional frameworks with different topologies. Complex (1) displays a new three-dimensional framework adopting a (3,3,6)-connected 3-nodal net with point symbol {4.62}2{42.610.83}. Complexes (2) and (3) are isomorphous and have a two-dimensional layered structure showing the same 3,6L60 topology with point symbol {4.26}2{48.66.8}. Complex (4) is a two-dimensional structure incorporating short Ag...Ag argentophilic interactions and has a uninodal 4-connectedsql/Shubnikov tetragonal plane net with {44.62} topology. Complex (5) exhibits a novel three-dimensional framework and more suprisingly contains twofold interpenetrated honeycomb-like networks, in which the single net has a trinodal (2,3,5)-connected 3-nodal net with point symbol {63.86.12}{63}{8}. Complex (6) crystallizes in a trigonal crystal system with the space group R\bar 3 and possesses a three-dimensional polymeric structure showing a binodal (4,6)-connectedfshnet with the point symbol (43.63)2.(46.66.83). The effect of the counteranions on the formation of coordination polymers is discussed in this study.

scholarly journals Structural diversity induced by ligand geometry: From two-dimensional to three-dimensional coordination polymers with pyridine

2020 ◽  
pp. 174751982096816
Author(s):  
Fang-Kuo Wang ◽  
Shi-Yao Yang ◽  
Hua-Ze Dong
Keyword(s):  
Coordination Polymers ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Dimensional Structure ◽  
Layer By Layer ◽  
Two Dimensional ◽  
Guest Molecules ◽  
X Ray ◽  
Benzenedicarboxylic Acid ◽  
Benzenetricarboxylic Acid

Two coordination polymers with two-dimensional and three-dimensional structures are, {[Zn3(bdc)3(py)2]·2NMP}n (1) (H2bdc = 1,4-benzenedicarboxylic acid) and [Zn2(NO3−)(btc)(nmp)2(py)]n (2) (H3btc = 1,3,5-benzenetricarboxylic acid), synthesized by hot-solution reactions of Zn(NO3)2·6H2O, pyridine (py) and two different ligands in N-methylpyrrolidone (NMP). {[Zn3(bdc)3(py)2]·2NMP}n exhibits two-dimensional networks with trizinc subunits [Zn3(COO)6py2] stacking with a layer-by-layer alignment, and there are strong π–π interactions involving py from adjacent layers. [Zn2(NO3−)(btc)(nmp)2(py)]n has a three-dimensional structure containing two independent zinc ions, tetrahedral ZnO4 and octahedral ZnNO5. Based on X-ray studies, the coordination polymers {[Zn3(bdc)3(py)2]·2NMP}n (1) have a porous structure with NMP guest molecules. In contrast, X-ray studies revealed that coordination polymer [Zn2(NO3−)(btc)(nmp)2(py)]n (2) had a larger void that was inhabited by coordinated py and NMP. In addition, the form of the two coordination polymers changed from two-dimensional to three-dimensional with transformation of the ligand geometry.

scholarly journals Low-Zpolymer sample supports for fixed-target serial femtosecond X-ray crystallography

2015 ◽  
Vol 48 (4) ◽  
pp. 1072-1079 ◽  
Author(s):  
Geoffrey K. Feld ◽  
Michael Heymann ◽  
W. Henry Benner ◽  
Tommaso Pardini ◽  
Ching-Ju Tsai ◽  
...  
Keyword(s):  
Protective Antigen ◽  
Three Dimensional ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Fixed Target ◽  
X Ray ◽  
X Ray Crystallography ◽  
Transmission Electron ◽  
Linac Coherent Light Source ◽  
Efficient Alternative

X-ray free-electron lasers (XFELs) offer a new avenue to the structural probing of complex materials, including biomolecules. Delivery of precious sample to the XFEL beam is a key consideration, as the sample of interest must be serially replaced after each destructive pulse. The fixed-target approach to sample delivery involves depositing samples on a thin-film support and subsequent serial introductionviaa translating stage. Some classes of biological materials, including two-dimensional protein crystals, must be introduced on fixed-target supports, as they require a flat surface to prevent sample wrinkling. A series of wafer and transmission electron microscopy (TEM)-style grid supports constructed of low-Zplastic have been custom-designed and produced. Aluminium TEM grid holders were engineered, capable of delivering up to 20 different conventional or plastic TEM grids using fixed-target stages available at the Linac Coherent Light Source (LCLS). As proof-of-principle, X-ray diffraction has been demonstrated from two-dimensional crystals of bacteriorhodopsin and three-dimensional crystals of anthrax toxin protective antigen mounted on these supports at the LCLS. The benefits and limitations of these low-Zfixed-target supports are discussed; it is the authors' belief that they represent a viable and efficient alternative to previously reported fixed-target supports for conducting diffraction studies with XFELs.

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.

Metal Ion-Driven Assembly of Two New Coordination Polymers Constructed by Asymmetric Tricarboxylate and Imidazole-Containing Ligands: Syntheses, Crystal Structures, and Luminescent Properties

2015 ◽  
Vol 68 (1) ◽  
pp. 121 ◽  
Author(s):  
Wenlong Liu ◽  
Xueying Wang ◽  
Mengqiang Wu ◽  
Bing Wang
Keyword(s):  
Infrared Spectroscopy ◽  
Coordination Polymers ◽  
Metal Ion ◽  
Three Dimensional ◽  
Luminescent Properties ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
Hydrothermal Conditions ◽  
X Ray ◽  
Dimethyl Benzene

Two new coordination polymers, namely, {[Cd3(bpt)2(bimb)2]·2(H2O)}n (1) and [Zn3(bpt)2(bimb)2]n (2) (bpt = biphenyl-3,4′,5-tricarboxylate, bimb = 1,4-bis(1-imidazol-yl)-2,5-dimethyl benzene), have been obtained under hydrothermal conditions. Their structures have been determined by single-crystal X-ray diffraction analysis and further characterised by elemental analysis and infrared spectroscopy. Complex 1 exhibits a trinodal (4,4,4)-connected topology with Schläfli symbol of (4.62.83)4.(64.82). Complex 2 is also a three-dimensional structure and displays a (3,4,6)-connected topology with Schläfli symbol of (4.62)2.(42.66.85.102).(64.82). It is shown that the asymmetrically tricarboxylate can bear diverse structures regulated by metal ions. The photoluminescence behaviours of compounds 1 and 2 were also discussed.

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.

Synthesis, Characterization and Crystal Structure of Coordination Polymers Developed as Anion Receptor

2018 ◽  
Vol 273 ◽  
pp. 134-139
Author(s):  
M.A. Kadir ◽  
Christopher J. Sumby
Keyword(s):  
Coordination Polymer ◽  
Coordination Polymers ◽  
Cadmium Nitrate ◽  
Two Dimensional ◽  
Anion Receptor ◽  
Slow Evaporation ◽  
One Dimensional ◽  
X Ray ◽  
X Ray Crystallography ◽  
Good Potential

Reaction of diamide ligand, namelyN,N’-2,6-bis (4-pyridylmethyl) pyridine dicarboxamide (L) with cadmium nitrate and cadmium perchlorate has given rise to the formation of two types coordination polymers. Compound (CP1-Cd) with formula molecule {[Cd (L)2(H2O)2](NO3)2·6H2O}nis a one-dimensional coordination polymer while compound (CP2-Cd), with formula molecule {[Cd (L)2(H2O)2](ClO4)2·31⁄2H2O.CH3OH}n, is a two dimensional coordination polymer. These coordination polymers were preparedviaslow evaporation methods and completely characterized by combination of solid state techniques such as Fourier Transform Infrared (FTIR) spectroscopy, elemental analysis and X-ray crystallography. This study revealed that coordination polymers derived fromN,N’-2,6-bis (4-pyridylmethyl) pyridine dicarboxamide can accommodate anions with different sizes, showing good potential as anion receptor.

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.

A Co-MOF with a (4,4)-connected binodal two-dimensional topology: synthesis, structure and photocatalytic properties

2019 ◽  
Vol 76 (1) ◽  
pp. 23-29 ◽  
Author(s):  
Zhi-Xiang Wang ◽  
Hai-Xin Tian ◽  
Jian-Gang Ding ◽  
Bao-Long Li ◽  
Bing Wu
Keyword(s):  
Dicarboxylic Acid ◽  
Photoelectron Spectroscopy ◽  
Optical Band Gap ◽  
Three Dimensional ◽  
Supramolecular Architecture ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hydrogen Bond Interactions ◽  
Point Symbol

The Co-MOF poly[[diaqua{μ4-1,1,2,2-tetrakis[4-(1H-1,2,4-triazol-1-yl)phenyl]ethylene-κ4 N:N′:N′′:N′′′}cobalt(II)] benzene-1,4-dicarboxylic acid benzene-1,4-dicarboxylate], {[Co(C34H24N12)(H2O)2](C8H4O4)·C8H6O4} n or {[Co(ttpe)(H2O)2](bdc)·(1,4-H2bdc)} n , (I), was synthesized by the hydrothermal method using 1,1,2,2-tetrakis[4-(1H-1,2,4-triazol-1-yl)phenyl]ethylene (ttpe), benzene-1,4-dicarboxylic acid (1,4-H2bdc) and Co(NO3)2·6H2O, and characterized by single-crystal X-ray diffraction, IR spectroscopy, powder X-ray diffraction (PXRD), luminescence, optical band gap and valence band X-ray photoelectron spectroscopy (VB XPS). Co-MOF (I) shows a (4,4)-connected binodal two-dimensional topology with a point symbol of {44·62}{44·62}. The two-dimensional networks capture free neutral 1,4-H2bdc molecules and bdc2− anions, and construct a three-dimensional supramolecular architecture via hydrogen-bond interactions. MOF (I) is a good photocatalyst for the degradation of methylene blue and rhodamine B under visible-light irradiation and can be reused at least five times.

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