scholarly journals Biomimetic resorcinarene-based copper(II) complex

2014 ◽  
Vol 70 (a1) ◽  
pp. C1374-C1374
Author(s):  
Aleksandar Višnjevac ◽  
Jérôme Gout ◽  
Olivia Bistri-Aslanoff ◽  
Olivia Reinaud
Keyword(s):  
Active Site ◽  
Metal Ion ◽  
Spectroscopic Studies ◽  
Hydroxyl Groups ◽  
Residual Water ◽  
Amino Acid Residues ◽  
Tight Control ◽  
Guest Molecules ◽  
Group A ◽  
Solvent Molecules

"The synthesis, structural characterization, as well as the chemical activity studies of a Cu(II) ""bowl complex", based on the resorcin[4]arene scaffold with three imidazole-containing coordinating arms grafted at the large rim, is presented. This complex is a biomimetic model of a metalloenzyme active site where a cofacial triade of amino-acid residues holds the metal ion in the active site [1]. The trisimidazole ligand reacts with a stoichiometric amount of copper(II) perchlorate to produce a Cu(II) diperchloratocomplex 1. Spectroscopic studies revealed a 5-coordinate SBP environment for the Cu(II) center provided by three imidazole arms, and two extra donors, one embedded in the resorcinarene cavity, the other exposed to the solvent, in exo position. These two labile sites are occupied by either coordinating solvent molecules or residual water, and are readily displaced by carboxylate donors, the position of which (endo or exo) is under tight control of the bowl-cavity. The reaction of 1 with CH3COONa led to a formation of the Cu(II) acetatocomplex 2. Molecular structure of 2 features a rigidified resorcinarene bowl, which was constructed by the addition of the four methylene bridges between the eight hydroxyl groups of the octol precursor [2]. The isolated resorcinarene basket reveals an approximate, non-crystallographic, 4mm point symmetry, and can easily host small guest molecules. Three methylimidazole-containing coordination arms at the large rim coordinate the Cu (II) ion. Its coordination sphere is completed by two O atoms from the intra-cavity bound acetate. The electron donors form a distorted square pyramide, where one of the nitrogens is at the appical position. The endo-coordination of the acetate is supported by an extensive network of intramolecular C-H···O and C-H···π interactions. Complex 2 crystallizes in P21/c space group; a=32.3310 (4)Å, b=11.5490 (1)Å, c=21.6020 (2)Å, beta=102.281(3)0."

Square-grid coordination networks of (5,10,15,20-tetra-4-pyridylporphyrinato)zinc(II) in its clathrate with two guest molecules of 1,2-dichlorobenzene: supramolecular isomerism of the porphyrin self-assembly

2009 ◽  
Vol 65 (3) ◽  
pp. m139-m142 ◽  
Author(s):  
Rajesh Koner ◽  
Israel Goldberg
Keyword(s):  
Self Assembly ◽  
Metal Ion ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Coordination Networks ◽  
Guest Molecules ◽  
Square Grid ◽  
Supramolecular Isomerism ◽  
Self Assembled ◽  
Solvent Molecules

The title compound, (5,10,15,20-tetra-4-pyridylporphyrinato)zinc(II) 1,2-dichlorobenzene disolvate, [Zn(C40H24N8)]·2C6H4Cl2, contains a clathrate-type structure. It is composed of two-dimensional square-grid coordination networks of the self-assembled porphyrin moiety, which are stacked one on top of the other in a parallel manner. The interporphyrin cavities of the overlapping networks combine into channel voids accommodated by the dichlorobenzene solvent. Molecules of the porphyrin complex are located on crystallographic inversion centres. The observed two-dimensional assembly mode of the porphyrin units represents a supramolecular isomer of the unique three-dimensional coordination frameworks of the same porphyrin building block observed earlier. The significance of this study lies in the discovery of an additional supramolecular isomer of the rarely observed structures of metalloporphyrins self-assembled directly into extended coordination polymers without the use of external ligand or metal ion auxiliaries.

scholarly journals Spectroscopic studies on lipoprotein structure modification under oxidative stress

2011 ◽  
Vol 26 (3) ◽  
pp. 167-178 ◽  
Author(s):  
Andreia Tache ◽  
Simona-Carmen Litescu ◽  
Gabriel-Lucian Radu
Keyword(s):  
Free Radicals ◽  
Metal Ion ◽  
Structural Changes ◽  
Oxidation Process ◽  
Spectroscopic Studies ◽  
Oxidative Modification ◽  
Hydroxyl Groups ◽  
Oxidative Damages ◽  
Endogenous Antioxidant

Matrix assisted laser desorption–ionization time of flight (MALDI-ToF) and infrared techniques were used to study oxidative modification of low density lipoproteins (LDL), considered to have the key role in biological process that initiates and accelerates the development of cardiovascular disease. The early identification of lipoperoxidation products creates the opportunity of the efficient prevention of eventual oxidative damages. MALDI analysis of LDL subjected toin vitrooxidation process initiated by 2,2-azobis(2-amidinopropane) dihydrochloride revealed that some fragments of lipoprotein changed the molecular weight by 16 and 32 Da due to the oxygen or hydroxyl groups attachment, and peroxide or hydroperoxide formation, while Fourier Transformed Infrared studies proved that lipoprotein changes its protein secondary conformation from predominantlyα-helix in predominantlyβ-turn. The increase in free radicals concentration correlated to structural changes, and the presence of transitional metal ion, copper (II), in the oxidation process lead to an enhancing of the damaging effects of free radicals on lipoprotein substrate. It was shown that the toxic effects of oxidants are delayed by the presence of glutathione (10 mM), an endogenous antioxidant.

Metal complexes of a sexadentate ligand: The occurrence of some solvent clathrates

1966 ◽  
Vol 19 (7) ◽  
pp. 1165 ◽  
Author(s):  
LF Lindoy ◽  
SE Livingstone ◽  
TN Lockyer ◽  
NC Stephenson
Keyword(s):  
Infrared Spectra ◽  
Diffraction Data ◽  
Metal Ion ◽  
X Ray Diffraction ◽  
Guest Molecules ◽  
X Ray ◽  
Metal Atoms ◽  
Clathrate Compound ◽  
Solvent Molecules ◽  
Water Alcohol

Complexes of iron(II), cobalt(11), nicke1(II), and copper(II) with the sexadentate ligand 1,5-bis-[2-(2-pyridylmethyleneimino)-phenyl]-l,5-dithiapentane (sexa) have been prepared. The iron(II) and cobalt(11) compounds are low-spin while the nickel(II) compounds are high-spin. Evidence is produced to support the contention that the metal atoms are six-coordinate. Many of the complexes were obtained as clathrates containing one or more molecules of water, alcohol, dimethylformamide, or acetone. The infrared spectra indicate that these solvent molecules, which are not readily lost, are not coordinated to the metal ion. A thermogravimetric study of [Fe sexa][FeCl4]2,(CH3)2CO showed that one molecule of acetone is lost at 260� whereupon the complex begins to decompose. X-ray diffraction data show that this compound has a host framework of four molecules per unit cell; the structure contains cavities into which the acetone molecules fit. These guest molecules determine the type of structure adopted by the clathrate compound.

scholarly journals A non-canonical metal center drives activity of the Sediminispirochaeta smaragdinae metallo-β- lactamase SPS-1

2018 ◽  
Author(s):  
Zishuo Cheng ◽  
Jamie VanPelt ◽  
Alexander Bergstrom ◽  
Christopher Bethel ◽  
Andrew Katko ◽  
...  
Keyword(s):  
Binding Site ◽  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Kinetic Studies ◽  
Binding Pocket ◽  
Spectroscopic Studies ◽  
Metal Center ◽  
Spin Coupling ◽  
Metal Binding Site

ABSTRACTIn an effort to evaluate whether a recently reported putative metallo-β-lactamase (MβL) contains a novel MβL active site, SPS-1 from Sediminispirochaeta smaragdinae was over-expressed, purified, and characterized using spectroscopic and crystallographic studies. Metal analyses demonstrate that recombinant SPS-1 binds nearly 2 equivalents of Zn (II), and steady-state kinetic studies show that the enzyme hydrolyzes carbapenems and certain cephalosporins but not β-lactam substrates with bulky substituents in the 6-7 position. Spectroscopic studies on Co (II)-substituted SPS-1 suggest a novel metal center in SPS-1, with reduced spin coupling between the metal ions and a novel Zn1 metal binding site. This site was confirmed with a crystal structure of the enzyme. The structure shows a Zn2 site that is similar that that in NDM-1 and other subclass B1 MβLs; however, the Zn1 metal ion is coordinated by 2 histidine residues and a water molecule, which is held in position by a hydrogen bond network. The Zn1 metal is displaced nearly 1 Å from the position reported in other MβLs. The structure also shows extended helices above the active site, which create a binding pocket that precludes the binding of substrates with large, bulky substituents in the 6/7 position of β-lactam antibiotics. This study reveals a novel metal binding site in MβLs, and suggests that the targeting of metal binding sites in MβLs with inhibitors is now more challenging with the identification of this new MβL.

Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication

2019 ◽  
Vol 476 (21) ◽  
pp. 3333-3353 ◽  
Author(s):  
Malti Yadav ◽  
Kamalendu Pal ◽  
Udayaditya Sen
Keyword(s):  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Triosephosphate Isomerase ◽  
Catalytic Mechanism ◽  
Degradation Mechanism ◽  
Structural Basis ◽  
Conserved Residues ◽  
Phosphodiester Bond ◽  
Cyclic Dinucleotides

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

scholarly journals Combined Use of Structure Analysis, Studies of Molecular Association in Solution, and Molecular Modelling to Understand the Different Propensities of Dihydroxybenzoic Acids to Form Solid Phases

Pharmaceutics ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 734
Author(s):  
Aija Trimdale ◽  
Anatoly Mishnev ◽  
Agris Bērziņš
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structure Analysis ◽  
Crystal Structure Analysis ◽  
Molecular Association ◽  
Hydroxyl Groups ◽  
Solid Phases ◽  
Solvent Molecules ◽  
Dynamics Simulations

The arrangement of hydroxyl groups in the benzene ring has a significant effect on the propensity of dihydroxybenzoic acids (diOHBAs) to form different solid phases when crystallized from solution. All six diOHBAs were categorized into distinctive groups according to the solid phases obtained when crystallized from selected solvents. A combined study using crystal structure and molecule electrostatic potential surface analysis, as well as an exploration of molecular association in solution using spectroscopic methods and molecular dynamics simulations were used to determine the possible mechanism of how the location of the phenolic hydroxyl groups affect the diversity of solid phases formed by the diOHBAs. The crystal structure analysis showed that classical carboxylic acid homodimers and ring-like hydrogen bond motifs consisting of six diOHBA molecules are prominently present in almost all analyzed crystal structures. Both experimental spectroscopic investigations and molecular dynamics simulations indicated that the extent of intramolecular bonding between carboxyl and hydroxyl groups in solution has the most significant impact on the solid phases formed by the diOHBAs. Additionally, the extent of hydrogen bonding with solvent molecules and the mean lifetime of solute–solvent associates formed by diOHBAs and 2-propanol were also investigated.

Chemical and Spectroscopic Studies of the Binuclear Copper Active Site

1982 ◽  
pp. 263-290
Author(s):  
Richard S. Himmelwright ◽  
Nancy C. Eickman ◽  
Aloysius F. Hepp ◽  
Edward I. Solomon
Keyword(s):  
Active Site ◽  
Spectroscopic Studies ◽  
Binuclear Copper
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