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The detection of fluoride ions in a competitive environment often poses several challenges. In this work, we have designed and synthesized a coumarin functionalized fluorescein dyad (R3) which represents an ideal through bond energy transfer (TBET) fluorophore with the coumarin unit as donor and fluorescein unit as acceptor. The bichromophoric dyad demonstrates the detection of fluoride ions in the parts per billion (ppb) concentration level (22.8 ppb) with high selectivity via a TBET emission signal at 548 nm with a diagnostic bright yellow colour fluorescence output. Based on UV-visible, fluorescence, 1H NMR and DFT studies, it is shown that the fluoride ion induces the opening of the spirolactam ring of the fluorescein moiety and provides a π-conjugation link between the donor and acceptor units enabling a TBET phenomenon with a larger pseudo-Stokes shift of 172 nm. To the best of our knowledge, this is the first report where the fluoride ion is detected via a TBET signal between the coumarin and fluorescein units in a bichromophoric dyad.

The detection of hydroxylamine in an aqueous medium is challenging due to its very similar chemical reactivity to its nearest competitors such as hydrazine hydrate and primary amines. Moreover, the detection of hydroxylamine at neutral pH adds further complexity to the sensing phenomenon due to its poor reactivity in a neutral aqueous medium. In this work, we have presented a diphenyl imidazole benzaldehyde (DIB) probe which demonstrates the detection of hydroxylamine (HA) in micromolar concentrations with high selectivity in 5% DMSO phosphate buffer solution at pH 7.4 via a fluorescence "turn-on" signal. The interaction of hydroxylamine with the probe has been comprehensively studied by using fluorescence spectroscopy, proton NMR, FTIR, ESI-mass spectrometry and DLS measurements. The experimental results were further corroborated with the DFT studies. These results could pave the way toward the development of molecular indicators for hydroxylamine in chemical and biological platforms.

We explored the antibacterial potential (alone and combination) against multidrug resistant (MDR) Pseudomonas aeruginosa isolates KG-P2 using synthesized thieno[3,2-c]pyran-2-ones in combination with different antibiotics. Out of 14 compounds, two compounds (3g and 3l) abridged the MIC of tetracycline (TET) by 16 folds. Compounds was killing the KG-P2 cells, in time dependent manner, lengthened post-antibiotic effect (PAE) of TET and found decreased the mutant prevention concentration (MPC) of TET. In ethidium bromide efflux experiment, two compounds repressed the drug transporter (efflux pumps) which is further supported by molecular docking of these compounds with efflux complex MexAB-OprM. In another study, these compounds inhibited the synthesis of biofilm.

Detection of ions in chemical, biological and environmental samples has gathered tremendous momentum considering the beneficial as well as adverse effects of the ions. Generally, most of the ions are beneficial up to an optimum concentration, beyond which they are toxic to human health. However, most of the fluorescence-based ion sensors are only active in non-aqueous solution because of the low solubility of the sensor molecules in aqueous buffer medium. In the present work, we have demonstrated that encapsulation of an aqueous insoluble thiocarbonohydrazone-locked salicylidene-based macrocyclic ligand in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membranes allows the selective detection of Zn2+ in aqueous medium with approximately 3-fold enhanced efficiency compared to its efficiency in DMSO medium. We have further modulated the charge of the membrane surface by adding various concentrations of a negatively charged lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG), and showed that negative surface charge further enhances the Zn2+ sensing efficiency up to approximately 6-fold. This strategy opens up a new avenue of utilizing organic sensors to detect vital ions in aqueous medium.

The development of new approaches to improve screening, diagnosis, prevention and treatment of cancer is an area of intensive research. Breast cancer is one such widespread category of cancer among women which is the world’s second leading cause of cancer death universally. The objective of this study is to analyze the structural stability of different diseased mutants of HER2 protein as well as to find out the inhibitory effects of Ru-terpyridine over mutant HER2 protein. To accomplish the study insight, we have carried out using different computational tools. From our in silico study, we conclude that, after mutation at positions D769H and V777L in HER2 protein, it was proceeded to cancerous growth and it becomes destabilize, followed by the binding performance of the ruthenium terpyridine over mutant HER2 protein shows the inhibitory effect against HER2 protein-targeted breast cancer.

Like common cold and flu, SARC-CoV-2 virus spreads by droplets of sneezes or coughs which virus affects people of various age groups. Today, this virus is almost distributed all over the world. Since binding process plays a crucial role between host and receptor, therefore, we studied the molecules intended toward inhibition process through molecular docking and molecular dynamics simulation process. From the molecular docking study, it is noteworthy that remdesivir shows better binding affinity toward the main protease of SARS-CoV2 compared to other studied drugs. Within studied phytochemicals, carnosic acid shows better binding poses toward main protease of SARS-CoV2 among studied phytochemicals. The amino acid residues GLN110 and PHE294 were almost found in all the studied interactions of drugs and phytochemicals with main protease of SARS-CoV-2. Furthermore, the results show a larger contribution of the Van der Waals energies as compared to others like electrostatic energies suggesting that ligands at the binding pocket are predominantly stabilized by hydrophobic interactions. The conformational change during ligand binding was predicted from Gibbs free energy landscape analysis through molecular dynamics simulation. We observed that, there were two main free energy basins for both docked carnosic acid complex and for docked remdesivir complex, only one main free energy basin was found in the global free energy minimum region. Communicated by Ramaswamy H. Sarma

Analysis of structural and functional binding performance of proteins related to genetic basis of diseases is a measure challenge. Podocin protein is a member of flotillin, stomatin and prohibitin, which expressed in nephron tissue. Type 2 nephrotic syndrome (NPHS2) occurs due to mutation in podocin protein. In the present article we have evaluated the binding performance of podocin protein both native as well as mutant with different phytochemicals like aegeline and berberine. We found that aegeline shown better inhibitory effect as compare to berberine against type 2 nephrotic syndrome.

The recent advancements in biotechnology and biomarkers discovery are now refining many biological systems in disease and diagnostic. The growing demand of application of biosensors in the field of medical diagnostic is because of its high sensitivity and multifunctional performances by a single chip. Currently, biosensor is widely used in health care, particularly diagnosis of infectious diseases as the number of predicted deaths remains high, with the pandemics and epidemics hazards and antibiotics resistance to various pathogens. The current scenario of biosensor technologies has potential to convey bed-side diagnostics, which matches traditional standards with respect to cost, accuracy, and time. Nevertheless, constant refinement in the technology is needed in order to provide lab-on-chip rapid, affordable, and accurate diagnostic. In this chapter, the importance of biosensor to diagnose several infectious as well as pathogenesis diseases like malaria has been discussed. Previous studies have stated that both Plasmodium falciparum dihydrofolate reductase–thymidylate synthase (PfDHFR-TS) and P. falciparum heme detoxification protein (PfHDP) are promising biomarker targets for malaria. Herein, in-depth analysis underpinning molecular interaction of PfDHFR and PfHDP with heme is studied employing molecular docking approach. Various structure validation tools confirmed the reliability of the modeled structures. The binding energy was found to be −7.47 kcal/mol and −9.61 kcal/mol for docked PfHDP and heme and PfDHFR-TS and heme complexes, respectively. The binding energy and other parameters like intermolecular energy and electrostatic energy corroborated that heme could perform better sensing strength toward PfDHFR-TS.

Two chromofluorescent coumarin-functionalized salicylidene based probes (3a and 3b) have been synthesized and evaluated for selective detection of fluoride and cyanide ions. Probes 3a and 3b selectively detect fluoride ions in acetonitrile medium via H-bond interaction and subsequent deprotonation to elicit a distinct visual colour change from colourless to deep red with a significant enhancement in their emission intensity to “turn on” a yellow fluorescence. In addition, probe 3a could optically discriminate the presence of cyanide ions over other anions by a colour change from colourless to deep yellow with an enhancement of green fluorescence in aqueous-acetonitrile medium (1:1 v/v). Job’s plot experiments revealed a 1:2 binding stoichiometry between the probes and fluoride or cyanide ions. A detailed analysis of the binding characteristics of probe 3a with fluoride and cyanide ions have been further carried out by 1H NMR titration studies which indicates a good correlation between colorimetric, UV–vis and 1H NMR observations. These experimental results were further corroborated from the theoretical models using quantum chemical calculations.

A base-mediated carbocyclization study has been performed between two allowed Baldwin cyclization modes (6-exo-trig and 6-exo-dig) and it was found that 6-exo-trig cyclization was preferred over 6-exo-dig. Allyl cyanide was found to be suitable and efficient pronucleophile for this investigation and two sp2–sp2 transition-metal-free C−C bond formations took place in a single operation to yield two differently functionalized biaryl compounds.

We have studied different interactions on the basis of the NBO analysis of both conformer of creatinine by using density function theory method. The energy between donor of C1-C3 and acceptor of C2-N8 is 1.69 kcal/mol, donor of C1 - C3 and acceptor of N6 - C11 is 3.96 kcal/mol for amino isomer. However we found the energy difference between C1 - N 6 and C 2 - N9 is 3.90 kcal/mol, C2 - N6 and N7 - H8 is 2.42 kcal/mol and C3 - N7 and C2 - N9 is 3.61 kcal/mol. The occupancy for C1-C3, C1-H4,C1-H5 and C1-N6 are 1.98294,1.97219,1.97491 and1.98091 respectively for amino isomer. For imino isomer we found the occupancy for C1 - C3, C1 - H4, C1 - N6, C3- O11 are 1.97607, 1.97033,1.98459 and 1.99574 respectively. These interaction energies are responsible for stabilization and also some nonbonding interactions enhance the stability.We have studied different interactions on the basis of the NBO analysis of both conformer of creatinine by using density function theory method. The energy between donor of C1-C3 and acceptor of C2-N8 is 1.69 kcal/mol, donor of C1 - C3 and acceptor of N6 - C11 is 3.96 kcal/mol for amino isomer. However we found the energy difference between C1 - N 6 and C 2 - N9 is 3.90 kcal/mol, C2 - N6 and N7 - H8 is 2.42 kcal/mol and C3 - N7 and C2 - N9 is 3.61 kcal/mol. The occupancy for C1-C3, C1-H4,C1-H5 and C1-N6 are 1.98294,1.97219,1.97491 and1.98091 respectively for amino isomer. For imino isomer we found the occupancy for C1 - C3, C1 - H4, C1 - N6, C3- O11 are 1.97607, 1.97033,1.98459 and 1.99574 respectively. These interaction energies are responsible for stabilization and also some nonbonding interactions enhance the stability.

The synthesis of a covalently bonded new photoresponsive molecular capsule formed from two resorcin [4]arene cavitands by fourfold ether linkages using azobenzene subunits is reported. The new molecular capsule undergoes trans to cis isomerization upon irradiation with 365 nm light and can be reversed back from cis to trans form by means of exposure to visible light (530 nm) in benzene solution. The photo-switchable behaviour was also investigated by H-1 NMR spectroscopy which further substantiated the UV-vis experiment. The quantum chemical calculations both at PM6 as well as at the DFT (B97-D) level of approximation for various stereoisomers starting from all-trans to all-cis indicated an increasing flexibility of these molecular capsules. (C) 2016 Elsevier B.V. All rights reserved.

Both one pot and step wise synthesis of methyl 3,5-diaminothieno[3,2-c]pyridin-4-one-2-carboxylates 6 have been delineated by the reaction of 6-aryl-4-methylthio-2H-pyran-2-one-3-carbonitriles 3, methyl mercaptoacetate and hydrazine hydrate. During the stepwise synthesis, functionalized thieno[3,2-c]pyran-4-ones 4 were isolated and treated with hydrazine hydrate to afford the desired products. Analogously, condensation–cyclisation of 5 with hydrazine hydrate delivered identical products, thieno[3,2-c]pyridin-4-ones 6, in excellent yields. The structure of isolated product 6 was ascertained by spectroscopic and single crystal X-ray diffraction analyses.

Two chromofluorescent thiocarbonohydrazone receptors (4 and 5) functionalized with coumarin derivatives have been synthesized and evaluated for selective detection of fluoride ions. Receptor 4 selectively recognizes fluoride ions via H-bond interaction and subsequent deprotonation to elicit a distinct visual colour change from colourless to pink with a significant 20-fold enhancement in its emission intensity to “turn on” a blue fluorescent. In contrast, receptor 5 exhibited a visible colour change from colourless to deep red upon interaction with fluoride ions over other anions. Detailed analysis of the binding characteristics of these receptors with fluoride ions revealed a 1 : 1 binding stoichiometry at lower concentrations while higher concentrations led to a 1 : 2 binding stoichiometry between the receptor and fluoride ions. These experimental results were further corroborated with quantum chemical calculations.

A simple, efficient and economical synthesis of dimethyl 3-amino-5-(2-oxo-2-arylethyl)thiophene-2,4-dicarboxylates has been reported by ring opening of methyl 3-amino-6-aryl-4-oxo-4H-thieno[3,2-c]pyran-2-carboxylates by alkoxide ions. Pyranothiophenes have been obtained by the reaction of methyl thioglycolate and 6-aryl-4-methylthio-2H-pyran-2-one-3-carbonitriles in the presence of triethylamine. A one-pot multicomponent protocol for the synthesis of tetrasubstituted thiophenes has been developed by reaction of 6-aryl-4-methylthio-2H-pyran-2-one-3-carbonitriles and methyl thioglycolate in the presence of sodium methoxide in excellent yields. The structure of the isolated compound was confirmed by single crystal X-ray diffraction and spectroscopic studies.

We have reported a simple, unprecedented base promoted synthesis of 7-substituted-1-(2-cyano-phenyl/phenyl)-3-sec amino-4,5-dihydro-1H-benz[e]indene-1,2-dicarbonitriles by reaction of 2-oxo-4-sec amino-5,6-dihydro-2H-benzo[h]chromene-3-carbonitriles and 2-cyanomethyl-benzonitrile/phenyl-acetonitrile under basic conditions at 100 °C. This reaction involves ring opening of 2-oxo-4-sec amino-5,6-dihydro-2H-benzo[h]chromene-3-carbonitrile by a carbanion generated in situ from 2-cyanomethylbenzonitrile/phenyl-acetonitrile followed by oxidative cyclization to afford the desired product. Alternatively, reaction of 6-aryl-4-sec amino-2H-pyran-2-one-3-carbonitriles and 2-cyanomethyl-benzonitrile under basic conditions provides functionalized benzo[h]quinolines. The structure of the synthesized compound was confirmed by single crystal X-ray.

A series of thieno[3,2-c]pyrans were designed and synthesized by L-proline catalyzed reaction of 6-aryl/5,6-diaryl-4-methylthio-2H-pyrane-2-one-3-carbonitriles or 4-(methylthio)-2-oxo-5,6-dihydro-2H-benzo[h]chromene-3-carbonitrile and methylthioglycolate in good yields. These thieno[3,2-c]pyrans exhibit substituent dependent fluorescence. The 6-aryl-thieno[3,2-c]pyrans 3a–3e exhibit high fluorescence quantum yields (95%) with large Stokes shifts, whereas the 6,7-di-substituted-thieno[3,2-c]pyrans 3f–3h show poor fluorescence in solution and exhibit an aggregation-induced emission (AIE). Interestingly, fused 6,7-di-substituted-thieno[3,2-c]pyran is highly fluorescent in the solution state, which reveals that restricted intramolecular rotation is the cause for AIE in 3f–3h.

Both one pot and step wise synthesis of methyl 3,5-diaminothieno[3,2-c]pyridin-4-one-2-carboxylates 6 have been delineated by the reaction of 6-aryl-4-methylthio-2H-pyran-2-one-3-carbonitriles 3, methyl mercaptoacetate and hydrazine hydrate. During the stepwise synthesis, functionalized thieno[3,2-c]pyran-4-ones 4 were isolated and treated with hydrazine hydrate to afford the desired products. Analogously, condensation–cyclisation of 5 with hydrazine hydrate delivered identical products, thieno[3,2-c]pyridin-4-ones 6, in excellent yields. The structure of isolated product 6 was ascertained by spectroscopic and single crystal X-ray diffraction analyses.

A series of calix[4]arene based ditopic receptors possessing bipyridyl and hydrazone units have been synthesized and evaluated for ionic recognition. It has been observed that the synthesized derivatives function as allosteric receptors for simultaneous recognition of Co2+and F− ions through non-covalent interactions. Significant bathochromic shifts in the UV–visible spectrum with a profound colour change promise their use to engineer novel applications.

A series of novel calix[4]arene-based neutral semicarbazone and thiosemicarbazone receptors have been synthesized and characterized. The molecular receptor 4a recognizes HSO 4 - in preference to other anions (Cl−, Br−, I−, ClO 4 - , H 2 PO 4 - and PF 6 - ) through a 1:1 binding-stoichiometry.

We have reported a simple, unprecedented base promoted synthesis of 7-substituted-1-(2-cyano-phenyl/phenyl)-3-sec amino-4,5-dihydro-1H-benz[e]indene-1,2-dicarbonitriles by reaction of 2-oxo-4-sec amino-5,6-dihydro-2H-benzo[h]chromene-3-carbonitriles and 2-cyanomethyl-benzonitrile/phenyl-acetonitrile under basic conditions at 100 °C. This reaction involves ring opening of 2-oxo-4-sec amino-5,6-dihydro-2H-benzo[h]chromene-3-carbonitrile by a carbanion generated in situ from 2-cyanomethylbenzonitrile/phenyl-acetonitrile followed by oxidative cyclization to afford the desired product. Alternatively, reaction of 6-aryl-4-sec amino-2H-pyran-2-one-3-carbonitriles and 2-cyanomethyl-benzonitrile under basic conditions provides functionalized benzo[h]quinolines. The structure of the synthesized compound was confirmed by single crystal X-ray.

Electron donating or withdrawing substituents on the aryl ring of the acetophenones negatively affect the yields.

A new precursor 2-(1-cyano-2,2-bis(methylthio)vinyl)benzonitrile has been synthesized by the reaction of 2-cyanomethylbenzonitrile, carbon disulfide and methyl iodide under basic conditions. The reaction of 2-(1-cyano-2,2-bis(methylthio)vinyl)benzonitrile with various functionalized aryl/heteroaryl methyl ketones or acetone under basic conditions afforded 4-amino-3-aroyl/heteroaroyl/acetyl-2-methylsulfanylnaphthalene-1-carbonitriles in good yields through a (5C + 1C) annulation strategy; this involves sequential intermolecular, followed by intramolecular, C–C bond formation reactions. The structure of the product was confirmed by single crystal X-ray crystallography.

We have reported a microwave assisted base directed regioselective synthesis of partially reduced chromenes, isochromenes and phenanthrenes. Functionalized 4-(piperidin-1-yl)-5,6-dihydro-2H-benzo[h]-chromen-2-one-3-carbonitriles have been used as precursors, which on reaction with functionalized acetophenones in the presence of KOH in DMF under microwave irradiation yield (Z)-2-(2-aryl-5,6-dihydro-4H-benzo[f]isochromen-4-ylidene)acetonitriles. The use of NaH in DMF provides 3-aryl-1-(piperidin-1-yl)-9,10-dihydro phenanthrene-2-carbonitriles in excellent yield regioselectively. The use of cyclohexanone as a nucleophile source yields (Z)-2-(3,4,7,8-tetrahydro-1H-naphtho[2,1-c]chromen-6(2H)-ylidene)acetonitriles. The structure and geometry of isochromene have been proved without any ambiguity by single crystal X-ray diffraction.

A short introduction to the fundamental features and recent developments of supramolecular chemistry is presented besides defining scope and limitation of this review article. A brief overview about calix[n]arenes and especially resorcin[4]arenes and their conformationally rigid cavitands is given. Selected examples are presented to demonstrate the dependence of self-assembly of cavitands exhibiting different flexibility either due to their basic macrocycle or due to flexible receptor units commonly located at the o,o′-position of the resorcinarene ring. In addition, the process of self-assembly is also controlled by metal coordination geometry as shown by one example. The receptor units may also be connected at the methylene group of the cavitand as shown by one example. Examples of supramolecular architectures are presented utilizing the special features of 2,2′:6′,2″-terpyridine (terpy) metal-binding ligand. The synthesis and characterization of a metallo-supramolecular Zn-coordination cage with a diameter of 4–5nm based on a cavitand-terpy building block is presented in detail.

A new class of functionalized calix[4]arenes have been synthesized and evaluated for colorimetric detection of fluoride ions. The molecular receptor 4b selectively recognizes fluoride ions via H-bonds and subsequent deprotonation to elicit a distinct colour change from yellow to dark purple.