Crystalline inclusion compounds derived from bulky organosilicon hosts – design, synthesis, structure and stability

New organosilicon compounds 1–3 featuring bulky triphenylsilyl moieties attached to rigid linear or trigonal spacer units have been synthesized and demonstrated to act as clathrate hosts, yielding crystalline inclusion compounds mostly with apolar and aprotic dipolar guest molecules, while the nonbulky dimethylphenylsilyl or trimethylsilyl substituted analogous compounds 4 and 5, which were also synthesized, proved inefficient. X-ray crystal structures of the inclusion compounds 1·DMF (1:1), 1·pyridine (1:1), 2·1,4-dioxane (2:1), 2·pyridine (2:1), 2·p-xylene (2:1), 2·H₂O (2:1) as well as of the unsolvated compounds 2 and 5 are described, and thermal stability studies of selected clathrates are reported.     

The effect of terminal alkoxy chain on mesophase behaviour,optical property and structure of chiral liquid crystal compounds derived from (−)-menthol

Herein, we present the results of our extensive investigations on the synthesis and phase behaviour of nine novel (?)-menthol-based chiral liquid crystal compounds. They possess three phenyl rings and substituted with (?)-menthyl and varying length of n-alkoxy chains at one end. With the aim of exploring the fundamental relationships between molecular structural features and thermal properties, nine terminal n-alkoxy groups from ethoxy to n-octadecaneloxy group in even numbers have been used. A detailed characterisation of their properties was carried out. The characterisation results clearly illustrate that all the series compounds show the thermodynamically stable phases; the shorter chain homologues display only the BPI and N* phases, and the middle ones exhibit BPI, N* and S_A* phases while the longer chain members show the BPI, N* and S_C* phases. Besides, the BPI appeared in a narrow temperature range because of their thermodynamic disruption. Temperature range of the N* phase narrows when the length of the n-alkoxy tail increases. The reflection peak is shifted towards short wavelength region with increasing temperature due to the winding of the chiral nematic helix in the N* phase. Furthermore, their inherent reflection peak intensities of reflections were gradually weakened.     

Supramolecular synthons and pattern recognition in adenine amides – synthesis,structures and thermal properties

An effective method for the synthesis of novel adenine amides was developed and successfully implemented, leading to 4-propyloxy-N-(9H-purin-6-yl)benzamide (1) and 4-dodecyloxy-N-(9H-purin-6-yl)benzamide (2). The compounds were fully characterised by means of spectroscopic (¹H NMR, ¹³C NMR, FT-IR) and thermal (TG, DSC) analysis. The crystallographic analysis revealed that the formation of supramolecular chains relies on hydrogen bonding between amide functionalities. All supramolecular synthons found in the crystal structure of 1 were confirmed with the temperature-dependent IR method. The temperature-dependent IR method is useful in determining supramolecular interactions for compound 2, for which the crystal structure could not be obtained. A detailed analysis of temperature-dependent FT-IR spectra was used for the first time to identify the hydrogen bonds that exist in the solid state of our compounds; it can therefore be considered a promising method for the pattern recognition of hydrogen bonding in supramolecular chemistry.     

Non-symmetrical discotic liquid crystalline dimers: molecular design,synthesis and mesomorphic properties‡

The synthesis and mesomorphic properties of novel non-symmetrical discotic dimers have been investigated. Dimers have been prepared by the combination of electron-deficient (n-type) anthraquinone and electron-rich (p-type) triphenylene discotic monomers. The mesophases have been characterised using polarising optical microscopy, differential scanning calorimetry and X-ray diffraction. Most of the dimers have been shown to exhibit a rectangular columnar mesophase and one has a nematic columnar mesophase also. Charge transfer behaviour has been studied by UV–Vis spectroscopy.     

An in silico approach to design peptide mimetics based on docking and molecular dynamics simulation of EGFR–matuzumab complex

Epidermal growth factor receptor (EGFR) plays an essential role in anticancer therapy. Matuzumab is an antibody for the treatment of colorectal, lung and stomach cancer. Matuzumab binds efficiently to EGFR and blocks its phosphorylation. The recent clinical successes have established application of peptides for cancer treatment. The present contribution introduces an in silico approach to design peptides based on molecular dynamics simulation (MDs) of the matuzumab-EGFR complex in water environment. Moreover, principal component analysis has been used to select multiple conformations of the complex in MDs for designing the peptides. The paratope and epitope in each conformation of the complex were determined, and the alanine scanning was used to identify the hot spots of EGFR conformers. The conformations of the peptides were optimized using PEP-FOLD server and MDs. The selected conformations were analyzed in a docking study to realize the binding site of the EGFR. Finally, pharmokinetics properties of the peptides were calculated. The designed oligopeptides were EWRSYYYWH, YYYWHNEWN, YYYWHNEWS and HNHSRNYGS with a higher affinity to the EGFR relative to the previously reported peptides. The newly designed peptides were investigated for their in vivo toxicities on rats, and all of them were non-toxic.     

New ciprofloxacin–dithiocarbamate–benzyl hybrids: design,synthesis, antibacterial evaluation,and molecular modeling studies

Research on Chemical Intermediates - We designed and synthesized a series of new ciprofloxacin–dithiocarbamate–benzyl hybrids 5a–n as potential antibacterial agents. All of the...     

Structure and mechanism formation of polyelectrolyte complex obtained from PSS/PAH system: effect of molar mixing ratio, base–acid conditions, and ionic strength

Colloidal dispersions of polyelectrolyte complexes were prepared in aqueous solutions. We have used mixtures containing the strongly charged anionic polyelectrolyte sodium polystyrene sulfonate (PSS) and the weak cationic polyelectrolyte polyallylamine hydrochloride (PAH). Both polymers have the same molecular weight. The complexes were obtained by adding drop by drop a solution of the anionic polyelectrolyte to excess cationic polyelectrolyte. In these conditions, sodium polystyrene sulfonate and polyallylamine hydrochloride self-assembled in nanometer-range complexes; the self-assembly is driven by electrostatic interactions, as well as by entropy changes due to counterion release. The electrostatic interactions were controlled in several ways: by changing the C _PSS/C _PAH concentration ratio, by modifying the pH (and thus the protonation degree of polyallylamine hydrochloride), and by adding sodium chloride (screened interactions). Dynamic light scattering experiments demonstrated that the hydrodynamics radius of the polyelectrolyte complex increases, changing from soluble to insoluble complex formation, when some physicochemical parameters are increased: the concentration ratio between polyelectrolytes, the sodium chloride concentration, and pH. Zeta potential measurements, as a function of the C _PSS/C _PAH concentration ratio, as well as of pH and ionic strength, allow us to state that the resulting particles have a structure constituted by a neutral core surrounded by a positively charged shell. The polyelectrolyte complexes have globular shapes, as observed by electron microscopy.     

Novel glitazones as PPARγ agonists: molecular design,synthesis, glucose uptake activity and 3D QSAR studies

Background

An alarming requirement for finding newer antidiabetic glitazones as agonists to PPARγ are on its utmost need from past few years as the side effects associated with the available drug therapy is dreadful. In this context, herein, we have made an attempt to develop some novel glitazones as PPARγ agonists, by rational and computer aided drug design approach by implementing the principles of bioisosterism. The designed glitazones are scored for similarity with the developed 3D pharmacophore model and subjected for docking studies against PPARγ proteins. Synthesized by adopting appropriate synthetic methodology and evaluated for in vitro cytotoxicity and glucose uptake assay. Illustrations about the molecular design of glitazones, synthesis, analysis, glucose uptake activity and SAR via 3D QSAR studies are reported.

Results

The computationally designed and synthesized ligands such as 2-(4-((substituted phenylimino)methyl)phenoxy)acetic acid derivatives were analysed by IR, ¹H-NMR, ¹³C-NMR and MS-spectral techniques. The synthesized compounds were evaluated for their in vitro cytotoxicity and glucose uptake assay on 3T3-L1 and L6 cells. Further the activity data was used to develop 3D QSAR model to establish structure activity relationships for glucose uptake activity via CoMSIA studies.

Conclusion

The results of pharmacophore, molecular docking study and in vitro evaluation of synthesized compounds were found to be in good correlation. Specifically, CPD03, 07, 08, 18, 19, 21 and 24 are the candidate glitazones exhibited significant glucose uptake activity. 3D-QSAR model revealed the scope for possible further modifications as part of optimisation to find potent anti-diabetic agents.

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Hybrid π-conjugated polymers from dibenzo pentacyclic centers:precursor design,electrosynthesis and electrochromics

π-Conjugated polymers(CPs)represent one of the quite important and rapidly growing branches of flexible electrochromic materials.Electrosynthesized hybrid CPs employing dibenzo pentacycles(fluorenes,carbazoles,dibenzothiophenes,and dibenzofuran)as the backbones have received considerable attention owing to their special structures and interesting electrochromic performances.Recent studies show that polymers from these structures exhibit decent contrast ratios,favorable coloration efficiencies,low switching voltages,fast response time,excellent stability,and color persistence.Intrinsically,their electrochromic properties significantly depend on fine-tailoring of precursor monomer structures,and polymerization techniques and conditions.This review devotes to showing a clear picture of the research progress of dibenzo pentacycle-centered CPs via electrochemical polymerization,including fluorenes,carbazoles,dibenzothiophenes,and dibenzofuran-based hybrid electrochromic polymers.Critical influences of the tailored precursor structures on their electropolymerization and resultant polymer performances are highlighted,aiming at providing an insight for the development of novel fused ring-based polymer electrochromic materials.     

Water Soluble Nickel – metformin ternary complexes: Thermal,DNA binding and molecular docking studies

The Nickel (II) complexes [Ni(Cl)₂(metf)(o-phen)] (1), [Ni(Cl)₂(metf)(opda)] (2) , [Ni(Cl)₂(metf)(en)] (3) , [Ni(Cl)₂(metf)(2,2'-bipy)] (4) , (metf = metformin, o-phen = ortho-phenanthroline, opda = ortho-phenylenediamine, en = ethylenediamine, 2–2′ bipy = 2–2′ bipyridyl) were synthesized and characterized using LC–MS, elemental analysis, molar conductance measurements, TGA-DTA, IR spectroscopy, magnetic moment measurements and electronic spectroscopy. The central Ni²⁺ was found to be in octahedral geometry. The DNA interaction of these complexes have been studied by UV–visible absorption studies, fluorescence emission technique and viscosity measurement. The complexes showed absorption hyperchromism in UV–visible spectra with calf thymus DNA. The binding constants from UV–visible absorption studies were 7.42 × 10⁴, 0.74 × 10⁴, 3.19 × 10⁴, 5.9 × 10⁴ M⁻¹ for 1 , 2 , 3 and 4 , respectively and Stern-Volmer quenching constants from fluorescence studies were 0.16, 0.41, 0.23, 0.18, respectively. Viscosity measurements revealed that the binding of the complexes with DNA could be surface binding, mainly due to groove binding. The highest DNA cleavage activity of the complexes is recorded for complex 1 . The complexes were docked in to B-DNA sequence, 5′(D*AP*CP*CP*GP*AP*CP* GP*TP*CP*GP*GP*T)-3′ retrieved from protein data bank (PDB ID: 423D), using Discovery Studio 2.1 software. C Docker Intectraction energy of 1 , 2 , 3 and 4 complexes is 32.027, 31.427, 35.393 and 30.521 respectively. The highest docking score is seen for complex 3 .     

Synthesis,characterization, molecular and supramolecular structures of nickel(II) complexes derived from α-diketone and α-ketoaldehyde bisaroylhydrazones

A new series of nickel(II) complexes derived from symmetrical diacetyl bisaroylhydrazones [Ni(L¹-R)] and unsymmetric phenylglyoxal bisaroylhydrazones [Ni(L²-R)] have been prepared and characterized. X-ray crystal and molecular structures of [Ni(L¹-H)], [Ni(L¹-pCH₃O)] and [Ni(L¹-pNO₂)] have been determined. In these complexes, the Ni(II) is in a distorted square planar environment and the aroylhydrazone acts as dinegative tetradentate ligand forming a 5,5,5-tricyclic chelate ring. Reaction of [Ni(L¹-R)] with aqueous ammonia afforded the paramagnetic five coordinate [Ni(L¹-R)(NH₃)] while [Ni(L²-R)] gave the diamagnetic square planar [Ni(L²-R)(NH₃)] complexes. Reaction of [Ni(L¹-R)] complexes with imidazole gave the corresponding paramagnetic octahedral bis(imidazole) adducts. X-ray structures of both [Ni(L¹-H)(HIm)₂] and [Ni(L¹-pNO₂)(HIm)₂] suggest a distorted octahedral structure where the bisaroylhydrazone occupies the basal plane while the two imidazoles occupy the axial sites. The molecular units are associated together forming triple stranded helical chains. With imidazole the [Ni(L²-R)] series gave the corresponding diamagnetic mono(imidazole) [Ni(L²-R)(HIm)] complexes, The X-ray structure of {Ni(L²-pCH₃)(HIm)] suggest square planar arrangement around the Ni(II) where the bisaroylhydrazone acts as dinegative NNO tridentate ligand forming with the Ni(II) a 5,6-bicyclic chelate ring the fourth coordination site is occupied by imidazole nitrogen.     

Synthesis, molecular structure and intramolecular aromatic-ring stacking interaction of a novel binuclear Cu(Ⅱ) complex with 1, 10-phenanthroline and phenylacetate

The complex [Cu(phen)2(POAc)3]ClO·4H2O has been synthesized and investigated by elemental analysis, IR spec-troscopy and X-ray diffraction methods, where phen = 1,10-phenanthroline, POAc = phenylacetate group). The complex crystallizes in the triclinic space group PI with two molecules in a unit cell of dimensions a = 1.0579(2) nm, b = 1.2423(3) nm, c = 1.9190(4) nm, α = 71.84(1)°, β = 80.50(2)°, γ = 88.60(1)°, V = 2.3625(9) nm3, R = 0.0407 and Rw = 0.0656. The complex results from bridging of two Cu(phen)2 units by three carboxylate groups, and each Cu2 ion is in a distorted square pyramidal geometry with two nitrogen atoms of phen and three carboxylate oxygen atoms of POAc. It has been showed that intramolecular stacking interactions occur between the phenyl moieties of POAc and aromatic rings of phen, leading to a novel molecule structure with two coordinating modes of carboxylate ligands, of which two phenylacetates are μ2-carboxylate-O-bridging ligands, and the other is a μ2-carboxylate-     

How do trehalose, maltose, and sucrose influence some structural and dynamical properties of lysozyme? Insight from molecular dynamics simulations

The influence of three well-known disaccharides, namely, trehalose, maltose, and sucrose, on some structural and dynamical properties of lysozyme has been investigated by means of molecular dynamics computer simulations in the 37-60 wt % concentration range. The effects of sugars on the protein conformation are found to be relatively weak, in agreement with the preferential hydration of lysozyme. Conversely, sugars seem to increase significantly the relaxation times of the protein. These effects are shown to be correlated to the fractional solvent accessibilities of lysozyme residues and further support the slaving of protein dynamics. Moreover, a significant increase in the relaxation times of lysozyme, sugars, and water molecules is observed within the studied concentration range and may result from the percolation of the hydrogen-bond network of sugar molecules. This percolation appears to be of primary importance to explain the influence of sugars on the dynamical properties of lysozyme and water.     

How homogeneous are the trehalose, maltose, and sucrose water solutions? An insight from molecular dynamics simulations

The structural properties resulting from the reciprocal influence between water and three well-known homologous disaccharides, namely, trehalose, maltose, and sucrose, in aqueous solutions have been investigated in the 4-66 wt % concentration range by means of molecular dynamics computer simulations. Hydration numbers clearly show that trehalose binds to a larger number of water molecules than do maltose or sucrose, thus affecting the water structure to a deeper extent. Two-dimensional radial distribution functions of trehalose solutions definitely reveal that water is preferentially localized at the hydration sites found in the trehalose dihydrate crystal, this tendency being enhanced when increasing trehalose concentration. Over a rather wide concentration range (4-49 wt %), the fluctuations of the radius of gyration and of the glycosidic dihedral angles of trehalose indicate a higher flexibility with respect to maltose and sucrose. At sugar concentrations between 33 and 66 wt %, the mean sugar cluster size and the number of sugar-sugar hydrogen bonds formed within sugar clusters reveal that trehalose is able to form larger clusters than sucrose but smaller than maltose. These features suggest that trehalose-water mixtures would be more homogeneous than the two others, thus reducing both desiccation stresses and ice formation.     

Coordination chemistry of H-spirophosphorane ligands towards pentacarbonylchlororhenium(I) – synthesis,structure and catalytic activity of complexes

Synthesis of a group of carbonyl rhenium coordination compounds with hydrospirophosphorane ligands was carried out and described. Different symmetrical HP(OCH₂CH₂NH)₂ L1 , HP(OCH₂CMe₂NH)₂ L2 , HP(OC₆H₄NH)₂ L3 , and unsymmetrical ligands HP (OCMe₂CMe₂O)(OC₆H₄NH) L4 were found to coordinate to the rhenium center as bidentate P,N donor ligands yielding fac-[ReCl (CO)₃ Ln ], where n = 1 – 4. Furthermore, monodentate coordination was also observed in some cases, as was clearly presented in the case of [ReCl(CO)₂( L4- κ²P,N)( L4- κP)] complex. All of the complexes were characterized using optical spectroscopy. Single-crystalX-ray diffraction was also performed in the case of fac-[ReCl(CO)₃ L3 ], fac-[ReCl(CO)₃ L4 ], [Re(CO)₂( L2 )₂]Cl and [ReCl (CO)₂( L4- κ²P,N)( L4- κP)] samples. Complexes [ReCl(CO)₃ L3 ] and [ReCl (CO)₃ L4 ], both bearing rings of conjugated double bonds within hydrospirophosphorane ligands, exhibited luminescence. Catalytic properties of rhenium complexes were assessed using the representative fac-[ReCl (CO)₃ L2 ] complex in the dimerization reaction of terminal alkynes. An efficient and selective procedure for synthesis of the E - enynes was developed. Coupling of (2-chlorophenyl)acetylene was mediated by [ReCl (CO)₃ L2 ]/TBAF system with a 100% conversion rate. Different substituents within aromatic alkynes were tolerated and the resulting products were dependent on the nature of the substituents.     

Design,preparation and applications of gel nanocomposites from bile acids – A brief review

Synthesis of advanced hybrid materials formed by the unification of nanoparticles with gels is gaining importance due to their unusual properties coupled with the ease of fabrication. The gel medium provides a template for generating complex inorganic nanostructures with controlled size and desirable mechanical properties. In this paper, we review the synthesis of various inorganic nanoparticles in gel matrices formed by the self-assembly of bile acid-derived gelators and the role of the gel medium to improve the properties of the nanocomposites.     

Structural design, solid-phase synthesis and activity of membrane-anchored β-secretase inhibitors on Aβ generation from wild-type and Swedish-mutant APP

Covalent coupling of β-secretase inhibitors to a raftophilic lipid anchor via a suitable spacer by using solid-phase peptide synthesis leads to tripartite structures displaying substantially improved inhibition of cellular secretion of the β-amyloid peptide (Aβ). Herein, we describe a series of novel tripartite structures, their full characterization by NMR spectroscopy and mass spectrometry, and the analysis of their biological activity in cell-based assays. The tripartite structure concept is applicable to different pharmacophores, and the potency in terms of β-secretase inhibition can be optimized by adjusting the spacer length to achieve an optimal distance of the inhibitor from the lipid bilayer. A tripartite structure containing a transition-state mimic inhibitor was found to be less potent on Aβ generation from Swedish-mutant amyloid precursor protein (APP) than from the wild-type protein. Moreover, our observations suggest that specific variants of Aβ are generated from wild-type APP but not from Swedish-mutant APP and are resistant to β-secretase inhibition. Efficient inhibition of Aβ secretion by tripartite structures in the absence of appreciable neurotoxicity was confirmed in a primary neuronal cell culture, thus further supporting the concept.     

Anti-inflammatory,analgesic and molecular docking studies of Lanostanoic acid 3-O-α-D-glycopyranoside isolated from Helichrysum stoechas

Helichrysum stoechas has been conventionally used as herbal tea due to its anti-inflammatory, antioxidant, antimicrobial and diuretic activities. Ethanolic extract of the aerial parts of the plant (HSE) afforded a lanostane triterpenoid glycoside. The isolated compound was characterized as Lanostan-3β-olyl-26-oic acid 3-O-α-D-glycopyranoside (HS-01) with the help of UV, IR, ¹H, ¹³C NMR and MS spectroscopic techniques. HSE (at 100 and 200 mg/kg doses) and the isolated compound, HS-01 (at 10 mg/kg dose) has been investigated for anti-inflammatory and analgesic activities against chemically challenged experimental animal. Both the HSE as well as HS-01 showed a substantial decline in paw volume when compared with the relevant control groups (p < 0.01 & p < 0.001). The HSE and HS-01 also confirms a significant prolongation of the paw licking or jumping towards the Eddy’s hot plate and reduction in quantity of writhes after the introduction of acetic acid in mice (p < 0.01 & p < 0.001). In order to have a better understanding of the binding interactions of HS-01 at molecular level, docking studies were performed with various macromolecular drug targets using AutoDock 4.2 and AutoDock Vina 1.1. Both programs predicted Galectin-3 as most favorable target for HS-01 followed by iNOS, whereas TNFα and COX-2 were among less favorable. Therefore, HS-01 could be developed as suitable therapy against inflammation and associated disorders.     

Excited-state molecular geometries of ClO2, O−3, St-3 and TiI4 determined from resonance Raman spectra

Resonance Raman band intensities for the υ₁ν₁ bands of some non-linear triatomic species (ClO₂, O⁻₃, and S^t-₃) and the tetrahedral molecule TiI₄ are analyzed in terms of an A-term scattering regime. It is demonstrated that excited-state molecular geometries can be determined, even in the absence of vibronically structured absorption spectra and excitation profiles, from the intensity distributions of overtone progressions, excited with different laser lines throughout the resonance region. Calculations of the bond length changes accompanying the lowest energy electric-dipole-allowed transitions are shown to be in accord with simple molecular orbital considerations.