Naresh Patwari Ganpathi

Indian Institute of Technology Bombay | IIT Bombay ·  Department of Chemistry

The dynamics of NO release upon photodissociation of nitroaromatic compounds is dependent on the nature of the interaction between the NO2 group and substituent in the ortho position. A bimodal (slow and fast) translational energy distribution of the NO photofragment indicates the presence of two distinct NO elimination channels. The slow-to-fast b...

Type IA topoisomerases maintain DNA topology by cleaving ssDNA and relaxing negative supercoils. The inhibition of its activity in bacteria prevents the relaxation of negative supercoils, which in turn impedes DNA metabolic processes leading to cell death. Using this hypothesis, two bisbenzimidazoles, PPEF and BPVF are synthesized, selectively inhi...

Antibiotic resistance via epigenetic methylation of ribosomal RNA is one of the most prevalent strategies adopted by multi-drug resistant pathogens. The erythromycin-resistance methyltransferase (Erm) methylates rRNA at the conserved A2058 position and imparts resistance to macrolides such as erythromycin. However, the precise mechanism adopted by...

Carboxylic acids form exceptionally stable dimers and have been used to model proton and double proton transfer processes. The stabilization energies of the carboxylic acid dimers are very weakly dependent on the nature of substitution. However, the electric field experienced by the OH group of a particular carboxylic acid is dependent more on the...

The velocity map imaging of the methyl radical formed by 266 nm photolysis of methyl iodide using 213 nm non-resonant multi-photon ionization (NRMPI) method. Comparison of the NRMPI method with the well-known (2+1) resonance multi-photon ionization (REMPI) method at 333.45 nm, which selectively probes Q-branch of band-origin transition of the methy...

The ability of phenol to transfer the proton to surrounding ammonia molecules in a phenol-(ammonia)n cluster will depend on the relative orientation of the ammonia molecules and a critical field of about 285 MV cm-1 is essential along the O–H bond for the transfer process. Ab-initio MD simulations reveal that for a spontaneous proton transfer proce...

The ability of phenol to transfer the proton to surrounding ammonia molecules in a phenol-(ammonia)n cluster will depend on the relative orientation of the ammonia molecules and a critical field of about 285 MV cm-1 is essential along the O–H bond for the transfer process. Ab-initio MD simulations reveal that for a spontaneous proton transfer proce...

Carboxylic acids form exceptionally stable dimers and have been used to model proton and double proton transfer processes. The stabilization energies of the carboxylic acid dimers are very weakly dependent on the nature of the substitution. However, the electric field experienced by the OH group of a particular carboxylic acid is dependent more on...

The 266 nm photodissociation of three xylene isomers and mesitylene leading to the formation of methyl radical was examined. The kinetic energy release profiles for the methyl radical were almost identical for all the three isomers of xylene and mesitylene, while substantial differences were observed for the corresponding profiles of the co-fragmen...

A velocity map imaging (VMI) spectrometer to investigate photodissociation dynamics was designed and fabricated. This spectrometer combines a skimmed molecular beam with a multi-stage time-of-flight mass spectrometer equipped with position-sensitive detection. Investigations on the 266 nm photodissociation of o-xylene leading to {sp2}C–C{sp3} bond...

Protein aggregation is a common and complex phenomenon in biological processes, yet a robust analysis of this aggregation process remains elusive. The commonly used methods such as centre-of-mass to centre-of-mass ( COM – COM ) distance, the radius of gyration ( R g ), hydrogen bonding (HB) and solvent accessible surface area (SASA) do not quantify...

The ability of phenol to transfer the proton to surrounding ammonia molecules in a phenol-(ammonia)n cluster will depend on the relative orientation of the ammonia molecules and a critical field of about 285 MV cm-1 is essential along the O–H bond for the transfer process. Ab-initio MD simulations reveal that for a spontaneous proton transfer proce...

The ability of phenol to transfer the proton to surrounding ammonia molecules in a phenol-(ammonia)n cluster will depend on the relative orientation of the ammonia molecules and a critical field of about 285 MV cm-1 is essential along the O–H bond for the transfer process. Ab-initio MD simulations reveal that for a spontaneous proton transfer proce...

The heterodimers of propargylbenzene (PrBz) with phenylacetylene (PHA) and monosubstituted fluorophenylacetylenes (FPHAs) were investigated using electronic and vibrational spectroscopic methods. The vibrational spectra in the acetylenic C–H stretching region show a marginal shift (0–4 cm–1) upon dimer formation, which suggests minimal perturbation...

The dissociation of HCl embedded in DMSO clusters was investigated by projecting the solvent electric field along the HCl bond using B3LYP-D3/6-31+G(d) and MP2/6-31+G(d,p) levels of theory. The B3LYP-D3 calculations reveal that the dissociation of HCl embedded in DMSO clusters requires a critical electric field of 138 MV cm–1 along the H–Cl bond. H...

The dissociation of HCl embedded in DMSO clusters was investigated by projecting the solvent electric field along the HCl bond using B3LYP-D3/6-31+G(d) and MP2/6-31+G(d,p) levels of theory. The B3LYP-D3 calculations reveal that the dissociation of HCl embedded in DMSO clusters requires a critical electric field of 138 MV cm–1 along the H–Cl bond. H...

The aggregates of monofluorinated phenylacetylenes in the gas-phase, investigated using the IR-UV double resonance spectroscopic method in combination with extensive structural search and electronic structure calculations, reveal the formation of liquid-like clusters with a π-stacked dimeric core. The structural assignment based on the IR spectra i...

Vibrational spectra of the methyl groups in mono-methylamine (MMA), dimethylamine (DMA), and trimethylamine (TMA) monomer and their clusters were measured in three experimental set-ups to capture their complex spectral features as a result of bend/umbrella-stretch Fermi resonance. Multiple bands were observed between 2800 and 3000 cm-1 correspondin...

The oxidation reaction of diorganotelluride R2Te, 1 (where R = C6H5NNC6H4) with NaIO4 resulted in the isolation of a telluroxane cluster, namely [(R2TeO)(μ-TeO2)(OTeR2)][TeO(OH)2], 2. The formation of 2 was confirmed by multinuclear (¹H, ¹³C and ¹²⁵Te) NMR and FT-IR spectroscopy, and elemental analysis. The structure of compound 2 was further corro...

The denaturation of human serum albumin (HSA) upon interaction with the surfactant sodium dodecyl sulphate (SDS) was examined by measuring the diffusion time of fluorophore (RITC) tagged HSA under near single-molecule conditions using fluorescence correlation spectroscopy. The diffusion time shows four distinct regions as a function of SDS concentr...

The appearance of multiple bands in the N–H stretching region of the infrared spectra of the neutral methylamine dimer and trimer is a sign of NH bend–stretch anharmonic coupling. Ab initio anharmonic calculations were carried out in a step-wise manner to reveal the origin of various bands observed in the spectrum of the methylamine dimer. A seven-...

Photoexcitation of van der Waals complexes can lead to several decay pathways depending on the complexation and the nature of the potential energy surfaces involved. Upon excitation of the chromophore, ionization of its weakly bound neighbor via energy transfer brings to light a unique relaxation process known as intermolecular Coulombic decay (ICD...

The rational design of conformationally controlled foldable modules can lead to a deeper insight into the conformational space of complex biological molecules where non-covalent interactions such as hydrogen bonding and π-stacking are known to play a pivotal role. Squaramides are known to have excellent hydrogen bonding capabilities and hence, are...

Electronic and vibrational spectroscopic investigations in combination with quantum chemical calculations were carried out to probe the formation of four sets of hetero-dimers of phenylacetylene with 2-fluorohenylacetylene, 3-fluorophenylacetylene, 4-fluorophenylacetylene and 2,6-difluorophenylacetylene. The interaction of phenylacetylene with fluo...

Ribose containing double-stranded nucleic acids exhibit helical structure, whereas sugar modified (xeno) nucleic acids may exhibit different structural features. The structural landscape of four stereo variants of furanosal nucleic acids and their C2′ deoxy counterparts, explored with molecular dynamics simulations, suggest that the configuration a...

Competing noncovalent interactions play a pivotal role in the folding and assembly of three-dimensional structures, especially in flexible molecules. Calculations using density functional theory reveal that two squaramide rings aggregate to form a slipped antiparallel π-stacked dimer with high propensity. This π–π stacking interaction is used to de...

Squaramide ring conjugated with Schiff‐bases decorated with hydroxy and methoxy functional groups differentially senses zinc and cadmium ions by turning on the fluorescence. The feebly emitting free ligands light‐up in the presence of zinc and cadmium acetates, wherein the acetate ion plays a pivotal role as a conjugate anion. The selective and dif...

The hydrogen‐bonded complexes of fluorophenylacetylenes exhibit unusual and interesting turn ON/FF fluorescence behaviour following excitation to 1 ππ* (S 1 ) state. The fluorescence switching behaviour can be realized either (i) changing the intermolecular structure, (ii) change in the position of fluorine substitution and (iii) change in the hydr...

Water and methanol are well known solvents showing cooperative hydrogen bonding, however the differences in the hydrogen bonding patterns in water and methanol is due to the presence of methyl group in methanol. The presence of methyl group leads to formation of C–H⸱⸱⸱O hydrogen bonds apart from the usual O–H⸱⸱⸱O hydrogen bonds. The electric fields...

The electric field experienced by the OH group of phenol embedded in the cluster of ammonia molecules depends on the relative orientation of the ammonia molecules, and a critical field of 236 MV cm-1 is essential for the transfer of a proton from phenol to the surrounding ammonia cluster. However, exceptions to this rule were observed, which indica...

Molecular dynamics simulations of benzene and 12 fluorobenzenes with various degrees of fluorine substitution in water reveal that the accumulation of water in the first solvent shell decreases with increase in number of fluorine atoms relative to benzene, with an exception of hexafluorobenzene. Further, the solute–solute radial density function in...

The potential of mean force for the dimers of fluorobenzenes sample both π-stacked and T-shaped structures for partially fluorinated benzenes viz., 1,4-difluorobenzene, 1,3,5-trifluorobenzene and 1,2,4,5-tetrafluorobenzene, and sample only the T-shaped structures for benzene and hexafluorobenzene. While, the free energy for the dimerization in wate...

The aggregation of phenylacetylene in the gas phase was investigated by selectively recording the IR spectra of the clusters consisting of up to six monomer units, which perhaps are the largest clusters of substituted benzene ever reported. Analysis of the IR spectra with aid of a B97-D3/aug-cc-pVDZ level calculations reveals the formation of anti-...

The structural transformation of double-stranded octameric xyloNA and RNA were probed by modulating the dispersion energy. For the RNA the increase and the decrease in dispersion energy leads to over-winind and unwinidng of the helix. These structural transformations resembles the features observed due to action of the enzymes topoisomerases and he...

The frequency shifts of donor stretching vibration in X-H···Y (X = C, N, O; Y = N, O) hydrogen-bonded complexes of phenylacetylene, indole, and phenol are linearly correlated with the electrostatic component of the interaction energy. This linear correlation suggests that the electrostatic component, which is the first-order perturbative correction...

The hydrogen-bonded complexes of aniline, 4-fluoroaniline and 4-ethynylaniline with ammonia, methylamine, dimethylamine, trimethylamine and triethylamine, were investigated using IR-UV double resonance spectroscopy. The formation of N–H···N hydrogen bonded complexes with anilines as donors and alkylamines as acceptors was inferred based on the appe...

The transmetalation reactions of mercury precursor, [Pentyl(N^C^N)HgCl] (19) with selenium halides (SeCl4, SeBr4, and SeCl2) were attempted to obtain the corresponding organoselenenium trichloride [Pentyl(N^C^N)SeCl3], tribromide [Pentyl(N^C^N)SeBr3], and monochloride [Pentyl(N^C^N)SeCl] respectively [(N^C^N) = 5-tert-butyl-1,3-bis-(N-pentylbenzimi...

The transmetalation reactions of mercury precursor, [Pentyl(N^C^N)HgCl] (19) with selenium halides (SeCl4, SeBr4, and SeCl2) were attempted to obtain the corresponding organoselenenium trichloride [Pentyl(N^C^N)SeCl3], tribromide [Pentyl(N^C^N)SeBr3], and monochloride [Pentyl(N^C^N)SeCl] respectively [(N^C^N) = 5-tert-butyl-1,3-bis-(N-pentylbenzimi...

Reactions of free tantalum cation, Ta+, and tantalum cluster cations, Tan+ (n = 2–10), with ammonia are presented. The reaction of monomer cation, Ta+, with two molecules of NH3 leads to formation of TaN2H2+ along with release of two H2 molecules. The dehydrogenation occurs until the formal oxidation number of the tantalum atom reaches +5. On the o...

The homodimers of singly fluorine substituted phenylacetylenes were investigated using electronic and vibrational spectroscopic methods in combination with DFT calculations. The IR spectra in the acetylenic C-H stretching region show a marginal red-shift for the dimers relative to the monomers. Further, the marginal red-shifts indicate that the ace...

The electric field experienced by an acid molecule in the acid-water cluster depends on its local environment comprising of surrounding water molecules. A critical field of about 193 and 163 MV cm(-1) is required for the dissociation of HCl and HBr, respectively, and is associated with the arrangement of water molecules around the acid. The critica...

The Double-Eight-Ring (D8R), an elusive Secondary-Building-Unit (SBU) of zeolites, has been stabilized for the first time both in solution and solid-state. The present study further establishes that any of the three double-ring building blocks of zeolites, viz. D4R, D6R, and D8R, ([ArPO3Zn(L)]n (n = 4, 6, or 8)) can be preferentially isolated (over...

The electric field experienced by a water molecule within a water cluster depends on its position relative to the rest of the water molecules. The stabilization energies and the red-shifts in the donor O-H stretching vibrations in the water clusters increase with the cluster size concomitant with the increase in the electric field experienced by th...

Three novel C 3-symmetric tris-salicylaldimine Schiff base based “off-on” fluorescence sensors have been designed and synthesized. The synthetic approach involves a simple imine bond (C = N) formation between 1,3,5-tris(4’-aminophenyl)benzene (TAPB) and 3,5-substituted salicylaldehydes. The presence of salicylaldehyde units on periphery of the tris...

The C-H∙∙∙N hydrogen-bonded complexes between several fluorophenyacetylenes with ammonia and methylamine were characterized by the red-shift in the acetylenic C-H stretching vibration of the phenylacetylene moiety. These red-shifts were linearly correlated with the stabilization energies calculated at CCSD(T)/CBS//MP2-aug-cc-pVDZ. Analysis of vario...

Expression of the genome rests primarily on proteins adopting folds in the specificity of their sequence code over side-chains. The underlying basis, despite intense scrutiny of the apparent code, remains largely unclear as a protein-folding problem. The interactions internal to the polypeptide main-chain are ubiquitous to folding but their contrib...

Structural variations in zinc phosphate cluster chemistry have been achieved through a careful selection of phosphate ligand, ancillary ligand, and solvent medium. The use of 4-haloaryl phosphates (X-dippH2) as phosphate source in conjunction with 2-hydroxypyridine (hpy) ancillary ligand in acetonitrile solvent resulted in the isolation of the firs...

The propargylbenzene dimer was investigated using mass selected electronic and infrared spectroscopy in combination with quantum chemical calculations. The IR spectrum in the acetylenic C-H stretching region indicates that the two propargylbenzene units in the dimer are in an almost identical environment. The stabilization energies calculated at va...

Quorum sensing is a cell density dependent phenomenon that utilizes inducers like γ-butyrolactones (GBLs) and their receptor proteins in Streptomyces species to control expression of a plethora of genes initiating antibiotic production and other secondary metabolic pathways. The receptor proteins regulate by binding to the DNA in the promoter regio...

Binary complexes of 2,6-difluorophenylacetylene with methylamine, dimethylamine, trimethylamine and triethylamine were investigated using one colour resonant two photon ionization and infrared-optical double resonance spectroscopic techniques combined with high level ab initio calculations. All four amines form CAc-HN hydrogen-bonded complexes. Add...

Binary complexes of 2,6-difluorophenylacetylene (DFPHA) with methylamine (MA), dimethylamine (DMA), trimethylamine (TMA) and tetramethylamine (TEA) were investigated using one colour – resonant two photon ionization and infrared-optical double resonance spectroscopic techniques combined with high level ab initio calculations. All the four amines fo...

The red-shifts in the acetylenic C–H stretching vibration of C–H∙∙∙X (X = O, N) hydrogen-bonded complexes increase with increase in the basicity of the Lewis base. Analysis of various components of stabilization energy suggests that the observed red-shifts are correlated with the electrostatic component of the stabilization energy, while the disper...

A fluorescent chemo-sensor, 1,3,5-tris(4'-(N,N-dimethylamino)phenyl)benzene was synthesized by substituting N-H protons of 1,3,5-tris(4'-aminophenyl)benzene with methyl groups. The chemo-sensor shows highly selective and remarkable fluorescence quenching in the presence of picric acid with detection limit of 1.5 ppm. The origin of the selectivity w...

Quorum sensing is a cell density dependant phenomenon that utilizes small molecule inducers like γ-butyrolactones (GBLs) and their receptor proteins for adaptation to the environment. The cognate GBLs that bind to several of this GBL receptor family of proteins remain elusive. Here, using CprB protein from Streptomyces coelicolor A3(2) as a model s...

A supramolecular fluorophore, 1,3,5-tris(4'-aminophenyl)benzene (TAPB), selectively senses polynitroaromatic compounds (PNAC), viz. 2,4,6-trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), picric acid (PA), m-dinitrobenzene (m-DNB) and p-dinitrobenzene (p-DNB) through donor-acceptor complexation. Steady-state and time resolved fluorescence measuremen...

We report the vibrational spectra of o-fluorophenylacetylene (OFPA), m-fluorophenylacetylene (MFPA), and p-fluorophenylacetylene (PFPA) in the electronically excited S1 and cationic ground D0 states. These new data show that relative location of the fluorine atom with respect to the acetylenic group can influence the transition energy and molecular...

It is demonstrated, using tandem mass spectrometry and ion trap, that pre-adsorption of a H2O molecule on the gold dimer cation, Au2+, enhances adsorption of CO and O2 molecules, which is otherwise inert towards these molecules. The rate of adsorption of CO on Au2(H2O)+ was found to be higher by two orders of magnitude relative to bare Au2+. The en...

The hydrogen-bonded complexes of phenylacetylene, 4-fluorophenylacetylene, 2-fluorophenylacetylene, and 2,6-difluorophenylacetylene with ammonia are investigated using IR-UV double resonance spectroscopy in combination with high-level ab initio calculations at the CCSD(T)/CBS level of theory. The CH⋅⋅⋅N hydrogen-bonded complex, which involves an i...

Phenylacetylene (PHA) consists of two substantially different subunits: the phenyl ring (aromatic) and the acetylenic (aliphatic) moiety. Both groups are represented by relatively high electron density caused by highly delocalized π-electron clouds. Here, we performed a detailed analysis of the phenylacetylene dimer which is characterized by a vari...

The hydrogen bonding behavior of trifluoromethylphenols and their water complexes were investigated using IR-UV double resonance spectroscopy. Both ortho- and meta-trifluoromethylphenols exist in the syn conformer, which is the global minimum in both the cases. The IR spectrum in the O-H stretching region reveals the absence of an intramolecular O-...

The hydrogen-bonded complexes of phenylacetylene, 4-fluorophenylacetylene, 2-fluorophenylacetylene and 4-cyanophenylacetylene with water were investigated using IR-UV double resonance spectroscopy. Phenylacetylene, 4-fluorophenylacetylene, 2-fluorophenylacetylene and 4-cyanophenylacetylene form quasi-planar cyclic complexes with water incorporating...

An enhancement in the excited state proton transfer (ESPT) processes of coumarin-102 (C-102) dye was observed upon addition of salicylic acid and hydrochloric acid in sodium dodecyl sulfate (SDS) micellar solution. The phenomenon was observed only in the micellar medium of anionic surfactant SDS and not in case of cationic (CTAB) or neutral (Tritio...

Alcohol complexes of 4-fluorophenylacetylene and 2-fluorophenylacetylene were investigated using IR-UV double resonance spectroscopy. Methanol forms a cyclic complex with both the fluorophenylacetylenes incorporating C-H···O and O-H···π hydrogen bonds, the structure of which is similar to that of the corresponding water complex but different from t...

The structure of the phenylacetylene-dimer has been elucidated using IR-UV double resonance spectroscopy in combination with high level ab initio calculations at the CCSD(T)/CBS level. The IR spectra in the acetylenic and the aromatic C-H stretching regions indicate that the two phenylacetylene moieties are in identical environments and very simila...

Small gold cluster cations, Au(n)(+), adsorb N(2) molecules effectively under multiple collision conditions. The saturation number for N(2) adsorption on a gold cluster cation depends on the number of dangling gold atoms and the triangular apexes. The saturation numbers were interpreted to arrive at the geometrical structures of gold cluster cation...

The IR-UV double resonance spectroscopy of phenylacetylene complexes with triazine, pyrazine and pyridine in the acetylene C-H group of phenylacetylene was investigated. These spectra indicate that in the complexes of triazine, pyrazine and pyridine the acetylenic group is minimally perturbed and the predominant interaction is with the π electron d...

Molecules with multiple hydrogen bonding sites offer the opportunity to investigate competitive hydrogen bonding. Such an investigation can become quite interesting, particularly when the molecule of interest has neither lone-pair electrons nor strongly acidic/basic groups. Phenylacetylene is one such molecule with three hydrogen bonding sites that...

Two distinct isomers for the binary complex between phenylacetylene and methylamine were observed. The first complex is characterized by the presence of a C-H···N hydrogen bond between the acetylenic C-H group and the N atom of methylamine. In the second complex the N-H group of methylamine interacts with the π electron density of the benzene ring...

The H(2)O and MeOH complexes of 2-(2'-pyridyl)benzimidazole (2PBI) were investigated using laser induced fluorescence and IR-UV double resonance spectroscopic techniques. The 0(0)(0) band for the S(1) <-- S(0) electronic transition of 2PBI was observed at 31,616 cm(-1), and corresponding transitions for the H(2)O and MeOH complexes show substantial...

The water complexes of 4-ethynylbenzonitrile (4EBzN) were investigated with IR-UV double resonance spectroscopy. Water interacts with the pi electron density of the C[triple bond]N group in 4EBzN, leading to the formation of a quasiplanar cyclic complex incorporating C-H...O and O-H...pi hydrogen bonds. The (H(2)O)(2) and (H(2)O)(3) complexes of 4E...

The structures of the binary complexes between phenylacetylene and several tertiary amines viz., triethylamine, 1-ethylpiperidine, 1-ethylpiperazine, 1-azabicyclo[2.2.2]octane, and 1,4-diazabicyclo[2.2.2]octane were inferred using infrared-optical double resonance spectroscopy. The IR spectra in the acetylenic C-H stretching region clearly rule out...