scholarly journals Multiaddressable molecular rectangles with reversible host–guest interactions: Modulation of pH-controlled guest release and capture

2015 ◽  
Vol 112 (3) ◽  
pp. 690-695 ◽  
Author(s):  
Alan Kwun-Wa Chan ◽  
Wai Han Lam ◽  
Yuya Tanaka ◽  
Keith Man-Chung Wong ◽  
Vivian Wing-Wah Yam
Keyword(s):  
Electrostatic Interactions ◽  
Computational Study ◽  
2D Nmr ◽  
Binding Mode ◽  
Ph Responsive ◽  
Guest Molecules ◽  
Square Planar ◽  
Metal Metal ◽  
Acids And Bases ◽  
Low Dimensional

A series of multiaddressable platinum(II) molecular rectangles with different rigidities and cavity sizes has been synthesized by endcapping the U-shaped diplatinum(II) terpyridine moiety with various bis-alkynyl ligands. The studies of the host–guest association with various square planar platinum(II), palladium(II), and gold(III) complexes and the related low-dimensional gold(I) complexes, most of which are potential anticancer therapeutics, have been performed. Excellent guest confinement and selectivity of the rectangular architecture have been shown. Introduction of pH-responsive functionalities to the ligand backbone generates multifunctional molecular rectangles that exhibit reversible guest release and capture on the addition of acids and bases, indicating their potential in controlled therapeutics delivery on pH modulation. The reversible host–guest interactions are found to be strongly perturbed by metal–metal and π–π interactions and to a certain extent, electrostatic interactions, giving rise to various spectroscopic changes depending on the nature of the guest molecules. Their binding mode and thermodynamic parameters have been determined by 2D NMR and van’t Hoff analysis and supported by computational study.

Synthesis and Structure of a Clathrated Two-Dimensional Metal-Organic Framework: [Cd(4,4'-bpy)2(H2O)2](ClO4)2·(L)2·H2O (L = Bis(1-pyrazinylethylidene)hydrazine)

2008 ◽  
Vol 73 (1) ◽  
pp. 24-31
Author(s):  
Dayu Wu ◽  
Genhua Wu ◽  
Wei Huang ◽  
Zhuqing Wang
Keyword(s):  
Metal Organic Framework ◽  
Channel Structure ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
Guest Molecules ◽  
X Ray ◽  
Square Planar ◽  
Metal Organic ◽  
Aqueous Meoh ◽  
Organic Framework

The compound [Cd(4,4'-bpy)2(H2O)2](ClO4)2·(L)2 was obtained by the reaction of Cd(ClO4)2, bis(1-pyrazinylethylidene)hydrazine (L) and 4,4'-bipyridine in aqueous MeOH. Single-crystal X-ray diffraction has revealed its two-dimensional metal-organic framework. The 2-D layers superpose on each other, giving a channel structure. The square planar grids consist of two pairs of shared edges with Cd(II) ion and a 4,4'-bipyridine molecule each vertex and side, respectively. The square cavity has a dimension of 11.817 × 11.781 Å. Two guest molecules of bis(1-pyrazinylethylidene)hydrazine are clathrated in every hydrophobic host cavity, being further stabilized by π-π stacking and hydrogen bonding. The results suggest that the hydrazine molecules present in the network serve as structure-directing templates in the formation of crystal structures.

scholarly journals Testing automatic methods to predict free binding energy of host–guest complexes in SAMPL7 challenge

2021 ◽  
Vol 35 (2) ◽  
pp. 209-222
Author(s):  
Dylan Serillon ◽  
Carles Bo ◽  
Xavier Barril
Keyword(s):  
Degrees Of Freedom ◽  
Binding Free Energy ◽  
Binding Mode ◽  
Specific System ◽  
New Host ◽  
Guest Molecules ◽  
Host Guest Complex ◽  
Automatic Methods ◽  
Material Sciences ◽  
Fundamental Direction

AbstractThe design of new host–guest complexes represents a fundamental challenge in supramolecular chemistry. At the same time, it opens new opportunities in material sciences or biotechnological applications. A computational tool capable of automatically predicting the binding free energy of any host–guest complex would be a great aid in the design of new host systems, or to identify new guest molecules for a given host. We aim to build such a platform and have used the SAMPL7 challenge to test several methods and design a specific computational pipeline. Predictions will be based on machine learning (when previous knowledge is available) or a physics-based method (otherwise). The formerly delivered predictions with an RMSE of 1.67 kcal/mol but will require further work to identify when a specific system is outside of the scope of the model. The latter is combines the semiempirical GFN2B functional, with docking, molecular mechanics, and molecular dynamics. Correct predictions (RMSE of 1.45 kcal/mol) are contingent on the identification of the correct binding mode, which can be very challenging for host–guest systems with a large number of degrees of freedom. Participation in the blind SAMPL7 challenge provided fundamental direction to the project. More advanced versions of the pipeline will be tested against future SAMPL challenges.

Computational study of the binding mode, action mechanism and potency of pregabalin through molecular docking and quantum mechanical descriptors

2021 ◽  
Vol 1199 ◽  
pp. 113200
Author(s):  
Lorena Meneses ◽  
Sebastian Cuesta Hoyos ◽  
Guillermo Salgado Morán ◽  
Patricio Muñoz C. ◽  
Lorena Gerli Candia ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Computational Study ◽  
Binding Mode ◽  
Quantum Mechanical ◽  
Action Mechanism

scholarly journals Crystal and molecular structure and 31P and 195Pt nmr spectroscopy of [Pt3S2(PMe2Ph)6][BEt4]2; a trinuclear complex containing triply-bridging sulphide ligands

1984 ◽  
Vol 62 (4) ◽  
pp. 696-702 ◽  
Author(s):  
Gordon William Bushnell ◽  
Keith Roger Dixon ◽  
Reiko Ono ◽  
Alan Pidcock
Keyword(s):  
Trinuclear Complex ◽  
Complete Analysis ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Metal Interactions ◽  
Nuclear Magnetic Resonance Spectra ◽  
Square Planar ◽  
Metal Metal ◽  
Pd Complexes

An X-ray diffraction study of [Pt3S2(PMe2Ph)6][BEt4]2 shows that it crystallises in the monoclinic space group, C2/c, with a = 15.447(2), b = 18.033(3), c = 26.505(5) Å, β = 96.73(2)°. The cation consists of three, distorted, square-planar cis-PtS2(PMe2Ph)2 moieties combined by sharing of the two sulphur atoms to produce a central Pt3S2 unit with C2 symmetry and Pt—Pt distances of 3.182(1) Å (one edge) and 3.108(1) Å (two edges). Complete analysis and computer simulation of 31P{1H} and 195Pt{1H} nuclear magnetic resonance spectra give values for 1J(Pt—P), 3202 Hz; 3J(Pt—P), −25 Hz; and 2J(Pt—Pt), 476 Hz. The structure is compared with previous results for analogous Ni and Pd complexes and the structural and nmr parameters are discussed with reference to the possibility of metal–metal interactions.

scholarly journals Novel Trimethine Cyanine Dye as Potential Amyloid Marker

2018 ◽  
Keyword(s):  
Absorption Spectra ◽  
Electrostatic Interactions ◽  
Amyloid Fibrils ◽  
Binding Mode ◽  
Docking Studies ◽  
Cyanine Dye ◽  
Dye Absorption ◽  
Self Association ◽  
A Chain ◽  
Log Normal

The applicability of the novel cyanine dye AK 3-1 to the detection and characterization of pathogenic protein aggregates, amyloid fibrils, was tested using the absorption spectroscopy technique. In an organic solvent dimethyl sulfoxide (DMSO), absorption spectra of AK3-1 exhibits vibrational structure with the relative intensity of 0-0 sub-band being higher than that for the 0-1 sub-band. In an aqueous phase the dye absorption band undergoes hypsochromic shift relative to DMSO due to H-aggregation of the dye. The interaction of AK3-1 with the native and fibrillar insulin was followed by the decrease of monomer band and the enhancement of H-dimer band. To evaluate the relative contributions of the monomeric and aggregated forms, the absorption spectra of the protein-bound dye were deconvoluted using the asymmetric log-normal (LN) function. The analysis of the set of fitting parameters provides evidence for the protein-induced AK3-1 self-association into the head-to-head dimers, with the magnitude of this effect being much more pronounced for fibrillar protein form. The molecular docking studies showed that the AK3-1 monomer tends to associate with the specific arrangement of side chains in the β-sheet formed by L17 leucine residues (of the insulin B-chain), located on the dry steric zipper interface of the fibril, while the dye dimers form stable complexes with the amyloid groove formed by the residues Q15 and E17 of the A-chain, and located on the wet interface of the fibril. The latter binding site is more easily accessible and is additionally stabilized by the electrostatic interactions between the positively charged dye and the E17 residue. This binding mode seems to be prevailing over that for the AK3-1 monomers. Based on the results obtained, AK3-1 may be recommended as a prospective amyloid marker complementary to the classical amyloid reporters Thioflavin T and Congo Red.

scholarly journals A Complete Assessment of Dopamine Receptor-Ligand Interactions through Computational Methods

2019 ◽  
Author(s):  
Beatriz Bueschbell ◽  
Carlos A.V. Barreto ◽  
Antonio J. Preto ◽  
Anke C. Schiedel ◽  
Irina S. Moreira
Keyword(s):  
Dopamine Receptor ◽  
Electrostatic Interactions ◽  
Specific Binding ◽  
Binding Pocket ◽  
Binding Mode ◽  
Receptor Subtypes ◽  
Receptor Ligand ◽  
Pi Stacking ◽  
Ligand Interactions ◽  
New Treatments

Background: Selectively targeting dopamine receptors has been a persistent challenge in the last years for the development of new treatments to combat the large variety of diseases evolving these receptors. Although, several drugs have been successfully brought to market, the subtype-specific binding mode on a molecular basis has not been fully elucidated. Methods: Homology modeling and molecular dynamics were applied to construct robust conformational models of all dopamine receptor subtypes (D1-like and D2-like receptors). Fifteen structurally diverse ligands were docked to these models. Contacts at the binding pocket were fully described in order to reveal new structural findings responsible for DR sub-type specificity. Results: We showed that the number of conformations for a receptor:ligand complex was associated to unspecific interactions > 2.5 Å and hydrophobic contacts, while the decoys binding energy was influenced by specific electrostatic interactions. Known residues such as 3.32Asp, the serine microdomain and the aromatic microdomain were found interacting in a variety of modes (HB, SB, π-stacking). Purposed TM2-TM3-TM7 microdomain was found to form a hydrophobic network involving Orthosteric Binding Pocket (OBP) and Secondary Binding Pocket (SBP). T-stacking interactions revealed as especially relevant for some large ligands such as apomorphine, risperidone or aripiprazole. Conclusions: This in silico approach was successful in showing known receptor-ligand interactions as well as in determining unique combinations of interactions, key for the design of more specific ligands.

scholarly journals Calix[4]arene-Based MOFs Controlled by Length of Alkyldiammonium Guests

2014 ◽  
Vol 70 (a1) ◽  
pp. C1713-C1713
Author(s):  
Ki-Min Park ◽  
Eunji Lee ◽  
Huiyeong Ju ◽  
Suk-Hee Moon ◽  
Shim Sung Lee
Keyword(s):  
Electrostatic Interactions ◽  
Three Dimensional ◽  
Van Der Waals Interactions ◽  
Supramolecular Interactions ◽  
Solvothermal Reaction ◽  
Guest Molecules ◽  
Structural Framework ◽  
Guest Species ◽  
Dimensional Network ◽  
Alternative Conformation

Our interest in the development of MOFs with the cavities controlled by guest species has led us to investigate the MOFs based on calix[4]arene derivatives, in which metal ions link the calix unit to give the networks with the cavities accommodating several guest species, because the calix[4]arene-based MOFs contain porosity associated with both the ligand itself and the structural framework. In the present work, we employed a low rim-functionalized calix[4]arene tetraacetic acid (H4CTA) with 1,3-alternative conformation as a multidentate building block and alkyldiamines as the guest molecules. In the solvothermal reaction of H4CTA and Zn(II) ion in the presence of alkyldiamines, two types of new MOFs based on calix[4]arene tetraacetate (CTA4-) depending on the lengths of α,ω–alkyldiammonium guests have been synthesized by including suitable alkyldiammonium guests. Their single-crystal X-ray diffraction analyses reveal that the short alkyldiammonium guests such as ethyldiammonium, propyldiammonium, and butyldiammonium lead to form two-dimensional framework with the cavity consisting of two CTA4-and four Zn(II) ions whereas the alkyldiammonium guests such as heptyldiammonium, octyldiammonium, nonyldiammonium, and decyldiammonium give rise to generate three-dimensional network with the cavity surrounded by six CTA4-and four Zn(II) ions. The alkyldiammonium guests in both MOFs are well accommodated by each cavity via a variety of supramolecular interactions including electrostatic interactions, hydrogen bonds and van der Waals interactions. We will present and discuss a study on the syntheses and characterization of two new MOFs based on calix[4]arene derivative.

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