Intercalation of anticancer drug Palbociclib with calf-thymus DNA: new insights from molecular spectroscopic, molecular dynamic simulations and cleavage studies

The interaction between the anti-cancer drug Palbociclib (PAL) and calf-thymus DNA (CT-DNA) was investigated using various biophysical techniques in a physiological buffer (pH 7.4). It was found that PAL intercalated into the base pairs of CT-DNA as evidenced from the results of UV-Vis, fluorescence, circular dichroism (CD), competitive binding assay with ethidium bromide (EB) and Hoechst 33258, KI quenching study, the effect of denaturing agent and viscosity measurements. The magnitude of binding constants (106 M-1) at different temperatures suggested strong binding between PAL and CT-DNA during complexation. The observed ΔHo > 0 and ΔSo > 0 indicated that the binding process is primarily driven by hydrophobic interactions. Molecular docking studies indicated partial intercalation of pyridopyrimidine ring between the base pairs of DNA. Free energy surface (FES) analysis derived from metadynamics simulation studies revealed the PAL-induced cleavage of DNA, which was confirmed by gel electrophoresis experiments.Communicated by Ramaswamy H. Sarma.

Spectroscopic and TD-DFT studies on the chromo-fluorogenic detection of cyanide ions in organic and aquo-organic media

A new naked-eye chromogenic and fluorogenic probe KS5 has been developed for the detection of CN- ions in neat DMSO and H2O:DMSO (1:1 v/v) media. The probe KS5 exhibited selectivity towards CN- and F- ions in organic and high selectivity towards CN- ions in aquo-organic media resulting in a colour change from brown to colourless and a turn-on fluorescence response. The probe could able to detect CN- ions via a deprotonation process, which was conceived by consecutive addition of hydroxide and hydrogen ions and confirmed using 1H NMR studies. The limit of detection (LOD) of KS5 towards CN- ions were in the range of 0.07-0.62 µM in both these solvent systems. Suppression of intra-molecular charge transfer (ICT) transition and photoinduced electron transfer (PET) process of KS5 by the added CN- ions are responsible for the chromogenic and fluorogenic changes observed, respectively. Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TD-DFT) calculations strongly supported the proposed mechanism along with the optical properties of the probe before and after the addition of CN- ions. To prove the practical applicability, KS5 was successfully utilized to detect CN- ions in cassava powder and bitter almonds as well as to determine CN- ions in various real water samples.

Spectroscopic and Theoretical Studies on the Selective Detection of Cyanide Ions by a Turn-On Fluorescent Chemo-Dosimeter and its Application in Living Cell Imaging

A new chemo-dosimeter AK4 containing quinoline fluorophore has rationally been designed, synthesised and characterized using 1H and 13C NMR and mass spectral techniques. The probe senses explicitly CN- ion through a dramatic enhancement in fluorescence over other commonly coexistent anions in H2O:DMSO (9:1 v/v) medium over a broad pH range (4-10). 1H NMR titration revealed the deprotonation followed by nucleophilic addition reaction of CN-, which was supported by 13C NMR and mass spectral examinations. The Job's continuous variation method indicated the formation of a 1:1 adduct between AK4 and CN- with a binding constant of 1.62 × 104 M-1. A limit of detection (LOD) towards CN- of 0.69 µM has been determined, which is much lower than the World Health Organization (WHO) recommended limit of CN- in drinking water (1.9 µM). The changes in the optical properties of AK4 upon reaction with CN- were delineated using Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TD-DFT) calculations. Moreover, fluorescence microscopic studies established that AK4 could be an effective probe for imaging intracellular CN- in HeLa cells.

Multi-Spectroscopic and TD-DFT Studies on Chromogenic and Fluorogenic Detection of Cyanide in an Aqueous Solution

Different spectroscopic techniques and Density Functional Theory (DFT)/Time-Dependent Density Functional Theory (TDDFT) calculations have been employed to investigate the dual channel CN- detection behaviour of the developed chemo-dosimeter (AK3). The CN- with AK3 reaction triggered a colour change from pale yellow to colourless and enhanced fluorescence. UV-Vis, fluorescence, 1H & 13C NMR and mass techniques coupled with theoretical calculations (Mulliken charges, dihedral angles) revealed that the CN- sensing process mechanism involves deprotonation of the N-H group followed by nucleophilic addition reaction. Detailed TD-DFT calculations showed that the relaxation of excited electrons from LUMO and to two different ground states is responsible for the weak/moderate fluorescence of AK3. Nucleophilic addition of CN- to the C-atom of the CH = CH bridge terminated the π-conjugation between donor and acceptor regions, reduced the coplanarity, decreased the ICT transition and consequently enhanced the fluorescence of the probe. The practical utility of the probe was demonstrated by detecting cyanide in food materials and determining CN- in environmental water samples.

Insilico molecular modelling to identify PDK-1 targeting agents based on its protein-protein docking interaction

PDK1, an attractive cancer target that downstreams 23 other kinases towards cell growth, survival and metabolism has gaining attention due to allosteric effect of ligands bound to it. Generally, the drug design strategy using pharmacophores is either a single protein structure or ensemble or ligand-based. Apart from these methods, yet another new approach of protein-protein docking with state of art computational tool like Schrodinger Suite to generate pharmacophores based on the interacting partners of the protein is proposed in this work. The structure-based pharmacophoric features were picked up from docking the ten interacting partners of PDK1 and screened against the Enamine libraries containing protein-protein interacting compound collection, advanced, protein mimetic and allosteric compounds. High throughput virtual screening against the PIF pocket of PDK1 yields an indole scaffold. The identified indole derivative is proposed to be a strong activator that binds in the protein-protein interaction site of PDK1 which was further confirmed by molecular metadynamics simulations, free energy surface analysis and MM-GBSA calculations. Thus, the pharmacophores generated by the interacting proteins for PPI can facilitate the virtual screening in structure-based drug discovery of similar therapeutic targets.Communicated by Ramaswamy H. Sarma.

Multi-spectroscopic, calorimetric and molecular dynamics evaluation on non-classical intercalation of antiviral drug Molnupiravir with DNA

The interaction of an antiviral drug Molnupiravir (MOL) with calf thymus DNA (CT-DNA) was investigated using a series of biophysical techniques. A significant hyperchromism with a blue shift  nm in the UV-Vis spectra indicated a high binding affinity of MOL for CT-DNA with binding constants in the order of 105 M-1. Competitive fluorescent dye displacement assays with ethidium bromide (EB) and Hoechst 33258 suggested an intercalative mode of binding of MOL with CT-DNA. Thermodynamic profiles determined using fluorescence titration and isothermal titration calorimetric (ITC) analysis matched well with each other. The negative free energy change revealed that the MOL/CT-DNA complexation is a spontaneous process. The negative values of enthalpy and entropy changes indicated that H-bonding and van der Walls interactions play dominant roles in stabilizing the complex. A decrease in viscosity of CT-DNA solution upon adding MOL indicated a partial intercalation mode of binding which was well supported by circular dichroism (CD) spectral and effect of KI and denaturation studies. Molecular docking and metadynamics simulation studies clearly showed the partial intercalation of the pyrimidine ring of MOL into the base pairs of DNA. Free energy surface (FES) contour indicated that the drug/DNA complex is stabilized by H-bonding and pi-pi/pi-cation interactions.Communicated by Ramaswamy H. Sarma.

Multi-spectroscopic, thermodynamic and molecular simulation studies on binding of pyrroloquinoline quinone with DNA: coexistence of intercalation and groove binding modes

The interaction between enzyme-like pyrroloquinoline quinone (PQQ) and calf-thymus DNA (CT-DNA) has been investigated by means of multi-spectroscopic (UV-Vis, fluorescence and circular dichroism), isothermal titration calorimetric (ITC), viscometry and molecular docking and metadynamics simulation techniques. Absorption spectral data suggested the formation of a PQQ/CT-DNA complex, which quenched the fluorescence of PQQ via the dynamic quenching process. The results of CD spectral studies coupled with viscosity measurements, competitive binding assays with Hoechst 33258 and ethidium bromide (EB), KI quenching experiments, gel electrophoresis and DNA melting studies indicated groove binding mode of interaction of PQQ with CT-DNA. ITC experiment revealed that the complex formation is a spontaneous process (ΔGo < 0) with a binding constant of 1.05 × 104 M-1. The observed ΔHo < 0 and ΔSo < 0 pointed out that the complex is stabilized by van der Waals forces along with H-bonding interactions. The outcomes of molecular docking and simulation studies confirmed the binding of PQQ with DNA. The free energy surface (FES) analysis pointed out the existence of an equilibrium between partial intercalation and groove binding modes, which is in good agreement with the competitive binding assays.Communicated by Ramaswamy H. Sarma.

Direct Adsorption of Graphene Oxide on a Glassy Carbon Electrode: An Investigation of Its Adsorption and Electrochemical Activity

Different modes of attachment of graphene oxide (GO) on an electrode surface resulted in unusual catalytic behavior respective of attachment because of film thickness. The present work investigates the direct adsorption of GO to the surface of a glassy carbon (GC) electrode. Scanning electron microscopy images revealed that multilayers of GO get adsorbed on the GC substrate and the adsorption was limited by folding up of the GO sheets at their edges. π-π and hydrogen bonding interactions between the GO and GC substrate flagged the adsorption of GO. pH studies revealed that higher adsorption of GO was achieved at pH = 3 rather than at pH = 7 and 10. Even though the electroactive surface area of adsorbed GO (GO_ads) was not remarkable (0.069 cm²), upon electrochemical reduction of GO_ads (Er-GO_ads), the electroactive surface area was escalated to be 0.174 cm². Similarly, the R_CT of Er-GO_ads was boosted to 2.9 kΩ compared to GO_ads which is 19 kΩ. Open circuit voltage was recorded to study the adsorption of GO on the GC electrode. Multilayered GO best fitted with the Freundlich adsorption isotherm, and the Freundlich constants like n and K_F were found to be 4 and 0.992, respectively. The Freundlich constant "n" revealed the adsorption of GO on the GC substrate to be a physisorption process. Furthermore, the electrocatalytic performance of Er-GO_ads was demonstrated by taking uric acid as a probe. The modified electrode showed excellent stability toward the determination of uric acid.

A highly selective probe for fluorometric sensing of cyanide in an aqueous solution and its application in quantitative determination and living cell imaging

A simple fluorescent probe (KS4) containing multiple reaction sites (phenolic -OH, imine and C = C bonds) is successfully synthesized and characterized using 1H NMR, 13C NMR, mass and single crystal XRD techniques. KS4 exhibits high selectivity towards CN- over a wide range of common anions in H2O:DMSO (1:1 v/v) leading to an amazing turn-on fluorescence at 505 nm via deprotonation of the phenolic -OH group. The limit of detection (1.3 µM) for CN- was much below the standard (1.9 µM) set by the World Health Organization (WHO). Stoichiometry of the interaction between KS4 and CN- was ascertained as 1:1 by the Job's plot method and the binding constant was determined to be 1.5x104 M-1. Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TD-DFT) based theoretical insight has been appealed to understand the optical properties of KS4 before and after the addition of CN- ion. The probe shows respectable real-time applicability for qualitative detection of CN- in almond and cassava powder as well as quantification in real water samples with excellent recoveries (98.8 - 99.8%). In addition, KS4 is found to safe towards living HeLa cells and successfully applied to the detection of endogenous cyanide ions in HeLa cells.

Multi-spectroscopic and molecular simulation methods of analysis to explore the mode of binding of Mebendazole drug with calf-thymus DNA

UV-vis, fluorescence, circular dichroism (CD) and ¹H NMR spectroscopic techniques have been employed to explore the mode of binding of Mebendazole (MBZ) drug with calf thymus DNA (CT-DNA). UV-vis and fluorescence spectral studies suggested a complex formation between the drug and nucleic acid. The fluorescence of MBZ was found to enhance upon binding with CT-DNA through a ground state complex formation with K_b in the order of 10⁴ M^-1. The thermodynamic aspects indicated that the complex formation is a spontaneous process and an entropy-driven one. ΔH⁰ > 0 and ΔS⁰ > 0 revealed that hydrophobic interaction plays a dominant role in the stabilization of the complex. Competitive dye displacement assays with ethidium bromide (EB) and Hoechst 33258 dyes and viscosity measurements pointed out that MBZ binds with CT-DNA via intercalation mode, which is confirmed by CD and ¹H NMR spectral studies as well as denaturation studies. Molecular docking analysis could not match well with the experimental results. However, molecular simulation studies and the resultant free energy surface (FES) analysis clearly showed that the benzimidazole ring of MBZ intercalated between the base pairs of the nucleic acid, which is in excellent agreement with the results of the various biophysical experiments.

A closer look at the mode of binding of drug pemetrexed with CT-DNA

The interaction of antifolate drug Pemetrexed (PEM) with CT-DNA has been studied by UV-Vis, fluorescence and circular dichroism spectroscopic techniques. The results of these spectroscopic studies in combination with viscosity measurements, voltammetric and KI quenching studies suggested a less-common mode of binding of PEM with CT-DNA i.e. neither intercalation nor groove binding. Thus, metadynamic (MD) simulation is utilized to decipher the nature of binding of PEM with CT-DNA. Analysis of free energy surfaces obtained in MD simulation, reveals that PEM binds to the 3'- and 5'-ends of the DNA molecule. The thermodynamics of the interaction has been investigated by isothermal titration calorimetric experiment. The analysis shows that PEM binds with CT-DNA strongly with a binding constant of 2.6x109 M-1 and the process is found to be spontaneous (ΔG - 12.84 kcal/mol). Further, positive values of enthalpy (ΔH 6.09 cal/mol) and entropy (ΔS 43.1 cal/mol) changes indicate that the binding is an enthalpically unfavourable and, instead, entropically driven process.Communicated by Ramaswamy H. Sarma.

Molecular spectroscopic and molecular simulation studies on the interaction of oral contraceptive drug Ormeloxifene with CT-DNA

The interaction between oral contraceptive drug Ormeloxifene (ORM) and calf thymus DNA (CT-DNA) was studied using UV-Vis, fluorescence, circular dichroism (CD) and ¹H NMR spectral techniques under physiological buffer (pH 7.4). Competitive binding assays with ethidium bromide (EB) and Hoechst 33258, viscosity measurements, KI quenching studies, molecular docking and metadynamics simulation studies were also substantiated the spectroscopic results. ORM is found to binds in the minor groove of CT-DNA as evidenced by: (1) non-displacement of EB from EB/CT-DNA complex; (2) appreciable displacement of Hoechst 33258 from its CT-DNA complex; (3) slight alteration in the CD signal; (4) small shifts (Δδ < 0.033 ppm) without broadening in ¹H NMR signals and (5) the nearly equal extent of quenching of fluorescence of ORM by KI in the absence and presence of CT-DNA. Negative values of both enthalpy and entropy changes pointed out that the interaction between ORM and CT-DNA is governed mainly by H-bonding and van der Waals forces. Negative free energy change suggested a spontaneous interaction between ORM and CT-DNA. The free energy landscape of the binding process was computed using metadynamics simulation. The simulation study results disclosed that ORM binds to the minor groove of DNA through H-bonding and π-π stacking interactions. The results of molecular docking and simulation studies corroborate the available experimental data.

Multi-spectroscopic and free energy landscape analysis on the binding of antiviral drug remdesivir with calf thymus DNA

Remdesivir (REM) is an antiviral drug, which exercises its effect by targeting specifically RNA-dependent RNA polymerase. The interaction of REM with calf thymus DNA (CT-DNA) was investigated by multi-spectroscopic techniques (UV-Vis, fluorescence, circular dichroism and ³¹P NMR) in combination with different biophysical experiments and metadynamics simulation studies. UV-Vis and fluorescence spectroscopic analysis indicated formation of a complex between REM and CT-DNA, whose binding constant is in the order of 10⁴ M^-1. Competitive displacement assays with ethidium bromide (EB) and Hoechst 33258 shown that REM binds to CT-DNA via intercalation mode. Significant alteration in the band due to base stacking pairs at 274 nm in the circular dichroism spectrum, appreciable increase in relative viscosity of the biomolecule upon binding with REM and the results of potassium iodide quenching studies confirmed that REM intercalates into the base pairs of CT-DNA. Thermodynamic parameters revealed that the binding of REM to CT-DNA is a spontaneous process (ΔG⁰ < 0) and the main force which holds them together in the REM/CT-DNA complex is electrostatic interaction (ΔH⁰ < 0 and ΔS⁰ > 0). The up-field shift in the ³¹P NMR signal of REM on interaction with CT-DNA suggested that phenyl ring adjacent to the phosphate moiety of REM may involve in the intercalation process. This is well supported by the analysis of free energy surface landscape derived from metadynamics simulation studies.

Intercalation of diafenthiuron insecticide with calf thymus DNA: spectroscopic and molecular dynamics analysis

A series of biophysical experiments like UV-Vis, fluorescence, circular dichroism (CD), competitive displacement assays, voltammetric studies, viscosity measurements and denaturation effect and metadynamics simulation studies were performed to establish the mode of binding of diafenthiuron (DF) insecticide with calf thymus DNA (CT-DNA). Analysis of absorption and fluorescence spectra in Tris-HCl buffer of pH 7.4 indicates the formation of a complex between DF and CT-DNA and the binding constant of which is in the order of 10⁴ M^-1. Competitive displacement assay with ethidium bromide (EB) and Hoechst 33258 suggests that the most probable mode of binding of DF with CT-DNA may be via intercalation mode. The results of other experiments such as CD spectral studies, viscosity measurements and the effect of denaturation agent urea support the intercalation of DF with CT-DNA. Thermodynamic parameters (ΔH^o, ΔS^o and ΔG^o) reveal that hydrogen bonds (H-bonds) or van der Waals (vdW) force is the main binding force in the spontaneous interaction between DF and CT-DNA. Molecular dynamics (MD) simulation studies confirmed the intercalation of DF into the base pairs of CT-DNA.Communicated by Ramaswamy H. Sarma.

A highly selective and sensitive ratiometric fluorescent probe for quantitative detection of Al(III) in different natural matrices

Highly selective and sensitive assay of Al(III) using ratiometric fluorescence enhancement is reported in an aqueous solution. The probe (named as RS5) exhibits a red-shift of 54 nm upon binding with Al(III) ion. The significant enhancement response of RS5 at 481 nm is attributed to the formation of a 1:1 complex between the probe and Al(III), wherein RS5 acts as a tridentate NNN-donor ligand. The complexation process is ascertained by 1H, 13C and 27Al NMR and HR-MS spectral techniques. The binding constant of the complex is determined to be 1.3x105 M-1. The ratiometric change in fluorescence upon complexation with Al(III) is ascribed to increase in intramolecular charge transfer (ICT) transition along with chelation enhanced fluorescence (CHEF) processes. The probe can be applied for monitoring Al(III) in a pH range of 6 - 8. The limit of detection (LOD) of RS5 for the examination of Al(III) is found to be 0.3 µM. With an aim to understand the sensing behaviour of RS5, the optical properties of the probe and its Al(III) complex are investigated using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. The probe is successfully employed for the determination of Al(III), with very high recovery percentages, in natural matrices like deep well water, tap water, drinking water, pond water, river water, bovine serum albumin (BSA) solution and blood serum.

Spectroscopic and theoretical evidences for the surface binding of voglibose drug with DNA

Binding of voglibose (VOG), an alpha glucosidase inhibitor, with CT-DNA has been investigated using various spectroscopic techniques including UV-Vis, fluorescence and circular dichroism (CD) coupled with relative viscosity. Isothermal titration calorimetric studies have been used to calculate the thermodynamic parameters such as ΔH (0.0188 cal/mol), ΔS (63.3 cal/mol/K) and ΔG (-18.8 kcal/mol), which reveal that the binding is a spontaneous process and hydrophobic and H-bonding interactions play major roles in the binding process. Effect of ionic strength confirms the existence of hydrophobic interaction between VOG and CT-DNA. Competitive displacement assays with ethidium bromide (EB) and Hoechst 33258 suggest that VOG possibly binds on the surface of CT-DNA. Viscosity measurements also disclose that the binding could be mainly surface binding. Corroborating the experimental observations, metadynamics molecular simulation studies confirm that VOG binding on the surface of the DNA molecule through hydrophobic interactions and direct and water molecule mediated H-bonding.

Investigating binding of insecticide buprofezin to DNA by experimental and metadynamics simulation studies

Buprofezin (BUP) is an insecticide which belongs to the thiadiazine structural family and known to damage DNA in mice. Though its toxic effect on human is not known clearly, understanding the mechanism of interaction of BUP with DNA can prove useful when required. Multi-spectroscopic experiments such as UV-Vis, fluorescence, circular dichroism (CD) and ¹H NMR coupled with viscosity measurements, urea effect and voltametric studies were performed to ascertain the mode of binding of BUP with calf thymus DNA (CT-DNA). Analysis of UV-Vis and fluorescence spectra indicated the formation of a complex between BUP and CT-DNA. Other experiments such as competitive binding assays with ethidium bromide (EB) and Hoechst 33258, viscosity measurements, effect of urea, CD, voltammetric studies and ¹H NMR spectral analysis suggested that BUP intercalates into the base pairs of CT-DNA. All these results revealed that the binding mode of BUP with CT-DNA should be intercalation and the binding constant is in the order of 10⁴ M^-1. The ΔH^o < 0 and ΔS^o < 0 suggested that H-bonding or van der Waals force was the main binding force between BUP and CT-DNA. The proposed mode of binding of BUP with CT-DNA has been visualized using in silico molecular docking and metadynamics simulation studies, which showed that the phenyl ring of BUP binds to CT-DNA via π-π stacking interaction in addition to H-bond formation.Communicated by Ramaswamy H. Sarma.

Dual sensing of methionine and aspartic acid in aqueous medium by a quinoline-based fluorescent probe

A quinoline-based Schiff base sensor, 6-methyl-2-oxo-1,2-dihydro-quinoline-3-carboxaldehyde-4(N)-phenylsemicarbazone (6MPS), has been developed for selective sensing of methionine and aspartic acid in aqueous medium through "on-off-on" type selective detection of copper ion. Fluorescence imaging of 6MPS, 6MPSC, 6MPSCN, 6MPSC-met, 6MPSCN-met, 6MPSC-asp and 6MPSCN-asp has been successfully demonstrated, in which the sensing probes 6MPSC-met, 6MPSCN-met, 6MPSC-asp and 6MPSCN-asp displayed bright green fluorescence in both in vitro and in vivo live cells.

Concentration-dependent mode of binding of drug oxatomide with DNA: multi-spectroscopic, voltammetric and metadynamics simulation analysis

The interaction between antihistaminic drug oxatomide (OXT) and calf-thymus DNA (CT-DNA) has been investigated in a physiological buffer (pH 7.4) using UV-Vis, fluorescence, ¹H NMR and circular dichroism spectral techniques coupled with viscosity measurements, KI quenching, voltammetry and in silico molecular modeling studies. OXT binds with CT-DNA in a concentration-dependent manner. At a lower [Drug]/[CT-DNA] molar ratio (0.6-0.1), OXT intercalates into the base pairs of CT-DNA, while at a higher [Drug]/[CT-DNA] molar ratio (13-6), the drug binds in the minor grooves of CT-DNA. The binding constants for the interaction are found to be in the order of 10³-10⁵ M^-1, and the groove binding mode of interaction exhibits a slightly higher binding constant than that of intercalative mode. Thermodynamic analysis of binding constants at three different temperatures suggests that both these modes of binding are mainly driven by hydrophobic interactions (ΔH^o > 0 and ΔS^o > 0). Voltammetric investigations indicate that the electro-reduction of OXT is an adsorption controlled process and shifts in reduction peak potentials reiterate the concentration-dependent mode of binding of the drug with CT-DNA. The free energy landscape obtained at the all-atom level, using metadynamics simulation studies, revealed two major binding forces: partial intercalation and minor groove binding, which corroborate well with the experimental results.Communicated by Ramaswamy H. Sarma.

2-Aminophenols based Schiff bases as fluorescent probes for selective detection of cyanide and aluminium ions - Effect of substituents

Three Schiff base based probes are designed and synthesized by facile condensation of a commercially available fluorophore 2,6-diformyl-4-tert-butylphenol with 4-nitro-2-aminophenol (KP1), 2-aminophenol (KP2) and 4-tert-butyl-2-aminophenol (KP3) and are characterized using various spectral techniques. The probes exhibit high selectivity and sensitivity CN^- and Al(III) ions with striking fluorescent signaling responses in H₂O-DMSO (1:1, v/v) medium. The mechanism of the probes' detection of CN involves deprotonation of the phenolic OH group(s) followed by nucleophilic addition of CN^- onto imine C-atom. The ¹H NMR chemical shifts of the OH protons of 2-aminophenol moiety exhibits a linear correlation with the Hammett's substituent constants (σ_p), yielding a positive reaction constant (ρ). In KP1, the electron-withdrawing nitro substituent polarizes the imine bond to a larger extent than in KP2, resulting in easier addition of CN^- to imine C-atom. The electron releasing tert-Bu substituent in KP3 produces the opposite effect leading to a sluggish addition reaction. The separately populated HOMO and LUMO in KP1 and a relatively lower HOMO-LUMO energy gap indicate substantial intramolecular charge transfer (ICT) character, leading to weak fluorescence emission. The large reduction in HOMO-LUMO energy gap, in KP1, upon addition of cyanide is responsible for the greater enhancement in fluorescence with blue shift upon addition of CN^-. Formation of tetrahedral Probe-Al(III) complex prevents the isomerization of imine bond, leading to enhancement in fluorescence and contribution from chelation enhanced fluorescence. As these probes show very low limits of detection of these ions, their practical utility has also been demonstrated.

3-Hydroxy-2-naphthoic hydrazide as a probe for fluorescent detection of cyanide and aluminium ions in organic and aquo-organic media and its application in food and pharmaceutical samples

The commercially available fluorophore, 3-hydroxy-2-naphthoic hydrazide (RS2), has rationally been selected for the study, which displays a rapid fluorescent response and high sensitivity for CN^- and Al(III) ions in neat DMSO and H₂O-DMSO (1:1 v/v) media. The addition of CN^- to RS2 triggers an enhancement in fluorescence at 505 nm (green fluorescence), while the addition of Al(III) increases the fluorescence of the probe with a blue-shift of emission maximum by 25 nm (bluish-green fluorescence). The probe's action was investigated by ¹H NMR titrations that indicate deprotonation of OH and NH moieties by these ions. ²⁷Al NMR of RS2-Al(III) complex suggests an octahedral geometry for the complex. The sensitivity of the fluorescent-based assays in aq. DMSO medium, 0.8 µM for CN^- and 1.9 µM for Al(III) ions are far below the limits in the World Health Organization guidelines for drinking water. RS2 detects Al(III) by the chelation-enhanced fluorescence (CHEF) mechanism. Besides, RS2 was successfully applied to detect CN^- and Al(III) ions in food materials and pharmaceutical samples, respectively.

Spectroscopic Studies on the Interaction of Naphthyridines with DNA and Fluorescent Detection of DNA in Agarose Gel

Four new naphthyridine derivatives (R1-R4) possessing amino acid or boronic acid moieties have been synthesized and characterized using ¹H and ¹³C NMR, FT-IR, and mass spectral techniques. The mechanism of binding of these probes with calf thymus DNA (CT-DNA) has been delineated through UV-Vis, fluorescence, and circular dichroism (CD) spectral techniques along with thermodynamic and molecular docking studies. Small hypochromicity in absorption maximum of the probes without any shift in wavelength of absorption suggests groove binding mode of interaction of these probes with CT-DNA, confirmed by CD and 1H NMR spectral data competitive binding assay with ethidium bromide (EB). CT-DNA quenches the fluorescence of these probes via a static quenching mechanism. In the case of R1 and R4, the observed ΔH^o < 0 and ΔS^o > 0suggest that these probes interact with CT-DNA through H-bonding and hydrophobic interactions, while in the interaction of R2 and R3, van der Walls and H-boding forces are found to be dominant (ΔH^o < 0 and ΔS^o < 0). Results of molecular docking investigations corroborate well with that of spectral studies, and these probes bind in the minor groove of DNA. These probes are found to be effective fluorescent staining agents for DNA in agarose gel in gel electrophoresis experiment with sensitivity comparable to that of EB, and DNA amounts as low as 37.5 ng are visually detectable in the gel.

A simple organic probe for ratiometric fluorescent detection of Zn(II), Cd(II) and Hg(II) ions in aqueous solution via varying emission colours to distinguish one another

A bis (thiosemicarbazone) based probe has been synthesized and structurally characterized. The probe exhibits good selectivity towards Zn(II), Cd(II) and Hg(II) ions in an aqueous solution containing 95% water with ratiometric fluorescence changes. The modes of coordination of the probe with these metal ions and binding properties have been examined using different spectral techniques. The binding constants, determined using fluorescence titration data, are found to be 9.8 × 10³, 1.39 × 10⁵ and 2.03 × 10¹³ M^-1, respectively for Zn(II), Cd(II) and Hg(II) complexes. The high sensitivity of the probe has been demonstrated by the very low limit of detection i.e. 5.1, 3.4 and 0.51 μM for Zn(II), Cd(II) and Hg(II) ions, respectively. Different coordination mode of these metal ions with the probe has resulted in varying intra-ligand fluorescence (λ_em nm, Zn(II): 488, Cd(II): 470 and Hg(II): 578) among these metal complexes.

Multi-spectroscopic, voltammetric and molecular docking studies on binding of anti-diabetic drug rosigiltazone with DNA

The binding of an anti-diabetic drug rosiglitazone (RG) with calf-thymus DNA (CT-DNA) in physiological buffer (pH 7.4) has been investigated using various spectral techniques such as UV-Vis, fluorescence, ¹H NMR and circular dichroism (CD) coupled with viscosity measurement and molecular docking studies. The binding of RG with CT-DNA results in small hypochromism without any change in absorption maximum and fluorescence quenching with hardly any shifts in emission maximum suggesting groove binding mode of interaction. The binding constant is found to be 4.2 × 10² M^-1 at 298 K. Thermodynamic analysis reveal that the binding is spontaneous and H-bonding and van der Waals forces play predominant role in the binding of RG with CT-DNA. Competitive interaction between RG and ethidium bromide with CT-DNA, viscosity measurements, KI quenching, ¹H NMR and CD studies substantiate the prosed mode of binding. Voltammetric investigations suggest that the electro-reduction of RG is an adsorption controlled process and shift of reduction peak to more negative potential, with a binding constant of 3.4 × 10³ M^-1, validates the groove binding mode of interaction between RG and CT-DNA. Molecular docking reveals that RG binds in the minor groove of DNA and the dominating interaction forces are H-bonding and hydrophobic interactions.

Multi-site probe for selective turn-on fluorescent detection of Al(III) in aqueous solution: synthesis, cation binding, mode of coordination, logic gate and cell imaging

An easy to make organic probe (hereafter called as R) possessing multiple ligating sites have been synthesized and characterized using spectral techniques. The probe exhibits selective and sensitive turn-on fluorescence response with Al(III) in aqueous dimethylformamide (DMF) (1:1 v/v) solution. Fluorescence titration experiment shows that the probe binds with Al(III) with a 1:1 stoichiometry and a binding constant of 6.6 × 10⁴ M^-1.The mode of coordination of R with Al(III) has been established suing ²⁷Al and ¹H NMR studies and the results suggest formation of an octahedral complex been them. The suggested point of attachment of R with Al(III) corroborates well with Density Functional Theory (DFT) optimized structure and Mulliken charges computed. Chelation-enhanced fluorescence (CHEF) is proposed as the mechanism of enhancement of fluorescence upon addition of Al(III) to R. The probe detects Al(III) in aqueous solution with a detection limit of 0.2 μM, which is much lower than the permissible limit of Al(III) set by the World Health Organization (WHO).The probe works in a wide pH range (4-11) and thus makes it a suitable candidate for environmental and biological applications. The fluorescence signals of R were used to construct an INHIBIT molecular logic gate. The confocal fluorescence microscope experiments show that R could be employed as a fluorescent probe for detecting Al(III) in living cells.

A simple fluorophore-imine ensemble for colorimetric and fluorescent detection of CN- and HS- in aqueous solution

Colorimetric and fluorescent detection of cyanide and hydrogen sulfide ions has been effected using a simple organic probe in H₂O:DMSO (20:80, v/v) medium. The probe exhibits a colour change from pale-yellow to red upon addition of these analytes under normal light and fluorescent change from green to red under UV lamp. Other competitive ions show no observable colour or fluorescence change. The binding constants of cyanide and hydrogen sulfide ions with the probe determined using fluorescence titration data are found to be 2.1 × 10⁴ and 1.6 × 10⁴ M^-1, respectively. The probe fluorimetrically detects the analytes in a wide pH range (4-10). ¹H and ¹³C NMR studies suggest that the probe senses cyanide ion through deprotonation and nucleophilic addition mechanism and hydrogen sulfide ion via deprotonation mechanism. Detection limits of cyanide and hydrogen sulfide are determined to be 0.15 and 1 μM, respectively. The practical utility of the probe has been demonstrated by same dual mode detection of cyanide in food materials like bitter almond, cassava flour and sprouting potato.

Rational design and application of a fluorogenic chemodosimeter for selective detection of cyanide in an aqueous solution via excimer formation

A new quinone-benzothiazole imine based chemodosimeter (R) was rationally designed, synthesized and characterized using NMR and mass spectral techniques. The receptor colorimetrically senses cyanide in aq. HEPES buffer: DMF (2:8 v/v) solution with an instantaneous colour change from yellow to bluish green. An enhancement of fluorescence intensity at 429 nm with excimer formation is also observed after addition of cyanide to the receptor, which is accompanied with a colour change from yellow to blue under UV lamp. Nucleophilic addition of cyanide to imine C-atom inhibits intra-molecular charge transfer (ICT) transition, which is responsible for the excimer formation. This chemical reaction is confirmed by ¹H NMR titration. The receptor binds with two equivalents of cyanide with a binding constant of 5.55 × 10⁴ M^-1. The limit of detection (LOD) of cyanide by the receptor is found to be as low as 69 nM, which is much lower than the acceptable limit of cyanide in drinking water as set by the WHO (1.9 μM). Electrochemical studies support the termination of ICT transition upon addition of cyanide ion. Theoretical studies substantiate experimental findings and excimer formation. The receptor fluorometrically detects cyanide present in tap water and food materials such as cassava flour, almond and potato.

Spectroscopic investigations on DNA binding profile of two new naphthyridine carboxamides and their application as turn-on fluorescent DNA staining probes

Two new 10-methoxydibenzo[b,h][1,6]naphthyridine-2-carboxamide derivatives (R1 and R2) have been synthesized and characterized using different spectral techniques. The binding of these probes with DNA was investigated using spectral (Electronic, fluorescence, ¹H NMR and circular dichroism) and molecular docking studies. These probes exhibited a strong fluorescence around 440 nm upon excitation around 380 nm. Electronic and competitive fluorescence titration studies, in HEPES [(4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)] buffer/dimethyl sulfoxide (pH 7.4) medium, suggest that these probes bind strongly to DNA, which is substantiated by ¹H NMR study. The binding constants are calculated to be 5.3 × 10⁷ and 6.8 × 10⁶ M^-1 for R1 and R2, respectively. From the results of spectral studies, it is proposed that the mechanism of binding of these probes with DNA is through minor groove binding mode, which is further confirmed by circular dichroism and molecular docking studies. Initial cell viability screening using MTT (3-[4,5-methylthiazol-2-yl]-2,5-diphenyl-tetrazolium bromide) assay shows that normal Vero cells are viable towards these probes at nano molar concentration, which is the concentration range employed in the present study for DNA staining (IC₅₀ in the order of 0.023 mM). The enhancement in fluorescence intensity of these probes upon binding with DNA enables the staining of DNA in agarose gel in gel electrophoresis experiment. The sensitivity of these probes is comparable with that of ethidium bromide and DNA amounts as low as 4 nano gram are detectable.Communicated by Ramaswamy H. Sarma.

Selective chromogenic detection of cyanide in aqueous solution - Spectral, electrochemical and theoretical studies

A bisimidazole ensemble (R) possessing naphthoquinone as signaling unit is synthesized and characterized using ¹H and ¹³C NMR and LC-MS spectral techniques. Anion sensing behaviour of the receptor has been investigated using electronic and fluorescence spectral techniques. The receptor exhibits a striking colour change from yellow to brown selectively with cyanide in aqueous HEPES buffer-DMSO (1:1 v/v) medium with a detection limit of 1 μM. Job's continuous variation method suggests that the stoichiometry of the interaction is 1:2 (R:CN^-). The binding constant for receptor-cyanide complex was found to be 8.7 × 10² M^-1. The mechanism of detection of cyanide occurs via deprotonation of imidazole N-H protons, which is well supported by electrochemical study. DFT based theoretical calculations shows that the energy gap between HOMO and LUMO decreases from 3.3086 (in R) to 1.7799 eV (in R + CN^-), which is responsible for the red-shift observed in the UV-Vis spectrum of R upon addition of cyanide ions. The present quinone-bisimidazole based receptor shows few advantages over similar bisimidazoles reported elsewhere.

Cyanohydrin formation of quinone appended benzaldehyde as a tool for selective colorimetric detection of cyanide in aqueous solution in a wide pH range

A Novel chemosensor R possessing napthoquinone substituted benzaldehyde has been successfully designed, synthesized and characterized using NMR and mass spectral techniques. The receptor exhibits striking colour change from pale yellow to intense green with sodium cyanide in DMF-H₂O (80-20% v/v) in a wide range of pH (3-12). Based on the results of spectral (UV-Vis, fluorescence and NMR), electrochemical and kinetic studies a plausible mechanism has been proposed for the cyanide detection process. The mechanism of sensing of cyanide by R is through the formation of cyanohydrin in acidic, neutral and basic solutions, which is the novelty of the receptor. The pseudo-first-order rate constants for the formation of cyanohydrin are found to be 2.9 × 10^-3, 3.9 × 10^-3 and 4.6 × 10^-3 min^-1 at pH values 5, 7 and 10, respectively in DMF-H₂O (80-20% v/v) medium, supporting the ability of R to form cyanohydrin with equal ease in different pH values. The results of Job's continuous variation method indicates a 1:2 (R:CN^-) stoichiometry for the interaction. The only minor drawback with the receptor is the time taken to impart visible colour change with cyanide ion, which is not instantaneous.

An easy to make chemoreceptor for the selective ratiometric fluorescent detection of cyanide in aqueous solution and in food materials

A ratiometric fluorescent receptor selectively detects cyanide in aqueous solution and food materials via deprotonation of a phenolic hydroxyl group.