Dheeraj K. Singh

pH-dependent Raman study of pyrrole and its vibrational analysis using DFT calculations.

Raman spectra of pyrrole in aqueous medium at different pH values, 2.5, 5.5, 7.5 and 10.5 were recorded in the two spectral regions, 1,040-1,160 cm(-1) and 3,300-3,360 cm(-1) and pH dependence of the linewidth, peak position and intensity of the Raman bands corresponding to the ring breathing and symmetric nu(N-H) stretching modes were examined. A linear pH dependence of the peak positions for the ring breathing mode and a maximum at nearly neutral pH (7.5) for the symmetric nu(N-H) normal mode is observed, whereas the linewidth (FWHM) shows almost no variation with the change of pH. A slight decrease in the wavenumber position of the nu(N-H) mode at pH value >7.5 indicates that the influence of deprotonation is small, which results from a weak interaction between the reference molecule and the surrounding environment. The density functional theory (DFT) calculations were made primarily to obtain the optimized geometry and vibrational spectra of pyrrole in the ground electronic state using B3LYP functional and the highest level basis set 6-311++G(d,p). The assignments of the normal modes of pyrrole were made on the basis of potential energy distribution (PED). The calculations were also performed on protonated and deprotonated structures of pyrrole.

Adsorption and desorption of tyrosine kinase inhibitor erlotinib on gold nanoparticles

We investigated interfacial behaviors of erlotinib (EL) on gold nanoparticles (AuNPs) by means of Raman spectroscopy. The adsorption reactions and structures of EL on AuNP surfaces were examined by UV-Vis absorption spectroscopy and surface-enhanced Raman scattering (SERS). Density functional theory calculations were performed to estimate the energetic stabilities of the drug-AuNP composites. Among the binding units in EL, the acetylenic C≡C group was calculated to be the most strongly binding on the AuNP cluster atoms, consistent with the SERS spectra. The concentration-dependent SERS spectra indicated that ∼10(-5) M of EL exhibited the highest SERS signals. The attached EL appeared to desorb more efficiently with 2mM glutathione than with cell culture media. The lack of a strong SERS signal of EL in the dark-field microscopy images of AuNP-EL complexes suggested almost complete desorption of EL inside cells.

Raman scattering and DFT calculations used for analyzing the structural features of DMSO in water and methanol

We report the concentration dependent Raman spectra of neat dimethyl sulfoxide [(CH3)2SO, DMSO] and its binary mixtures with water (W)/methanol (M) in both ν(SO) and ν(C–H) regions. The ν(SO) line profile of neat DMSO was resolved into four component peaks at 1036, 1044, 1054 and 1064 cm−1 and assigned to different dimeric species of neat DMSO. A careful analysis of the Raman spectra of DMSO with water in the ν(SO) region at different concentrations reveals that upon dilution, an additional peak is observed at ~1017 cm−1 (lower side of the peak ~1036 cm−1) which is attributed to the hydrogen bonding of DMSO with water. For the highest dilution case (χ = 0.1 of DMSO), hydrogen bonded species and symmetric stretching of the dimeric ν(SO) mode were obtained which suggest that DMSO exists in dimer form even at low concentration of DMSO. The significant blue shifting of the C–H frequency due to C–H⋯O hydrogen bonding was also obtained in the case of both solvents. Our experimental results imply the existence of the dimer form of DMSO in neat as well as at χ = 0.1 of DMSO. In order to simulate and validate our experimental findings, detailed ab initio and density functional theory (DFT) calculations were also performed to obtain the ground state geometries of neat DMSO, self-associated dimer, trimer and their hydrogen bonded complexes with water and methanol. Our calculated structure of DMSO in dimer and trimer form reports a more accurate and stable geometry, in comparison to earlier calculation on these structures. Overall in this study nice spectra–structure correlations were obtained.

Molecular Structure and Interactions in the Ionic Liquid 1-Ethyl-3-methylimidazolium Trifluoromethanesulfonate

Quantum chemical theory (DFT and MP2) and vibrational spectroscopy (ATR-IR and Raman) were employed to investigate the electronic structure and molecular interactions in the room-temperature ionic liquid 1-ethyl-3-methylimidazolium trifluoromethanesulfonate. Various possible conformers of a cation-anion pair based on their molecular interactions were simulated in the gas phase. All the different theoretical (MP2, B3LYP, and the dispersion-corrected wB97XD) methods assume the same ion-pair conformation for the lowest energy state. Basis set superimpose error (BSSE) correction was also introduced by using the counterpoise method. Strong C-H···O interactions between the most acidic hydrogen atom of the cation imidazole ring (C2H) and the oxygen atom of the anion were predicted where the anion is located at the top of (C2H). In this case, methyl and alkyl groups also interact with the anion in the form of a C-H···O hydrogen bond. Interestingly, the dispersion-corrected methodology neglects the C4/C5-H···O and C-H···F interaction in the ion-pair calculations. The theoretical results were compared with the experimental observations from Raman scattering and ATR-IR absorption spectroscopy, and the predictions of the molecular interactions in the vibrational spectra were discussed. The wavenumber shifts of the characteristic vibrations relative to the free cation and anion are explained by estimating the geometric parameters as well as the difference in the natural bond orbital (NBO) charge density.

Colloidal gold nanoparticle conjugates of gefitinib.

Gefitinib (GF) is a US Food and Drug Administration-approved epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitor for treating the lung cancers. We fabricated colloidal gold nanoparticle (AuNP) conjugates of the GF anticancer drug by self-assembly to test their potency against A549, NCI-H460, and NCI-H1975 lung cancer cells. GF adsorption on AuNP surfaces was examined by UV-vis absorption spectra and surface-enhanced Raman scattering. Density functional theory calculations were performed to estimate the energetic stabilities of the drug-AuNP composites. The N1 nitrogen atom of the quinazoline ring of GF was calculated to be more stable than the N3 in binding Au cluster atoms. The internalizations of GF-coated AuNPs were examined by transmission electron and dark-field microscopy. A cell viability test of AuNP-GF conjugates with the EGFR antibody exhibited much higher reductions than free GF for A549, NCI-H460, and NCI-H1975 lung cancer cells after treatment for 48.

Diversity of endophytic mycobiota of tropical tree Tectona grandis Linn.f.: Spatiotemporal and tissue type effects

Fungal endophytes were isolated from leaf, bark and stem of Tectona grandis Linn.f. sampled at four geographical locations in winter, summer and monsoon seasons. The recovered 5089 isolates were assigned to 45 distinct morphotypes based on morphology. The sequences of the internal transcribed spacers (ITS) of the nrDNA of some morphotypes were identical, but morphological differences were strong enough to consider these morphotypes as separate species. Forty-three morphotypes were assigned to ascomycotina and two to basidiomycotina. Ascomycotina was the predominating group with 99.7% of total isolates followed by basidiomycotina with only 0.3% of total isolates. Diaporthe (Phomopsis) species dominated the communities independently on tissue type, location or season. More than 60% of the examined tissue pieces were colonized by members of this species complex. While these endophytes are ubiquitous others were tissue or location specific. Tissue type had the strongest effect on the species evenness of the endophytic assemblage followed by geographical location and season. However, Shannon-Wiener index (H’) significantly (p ≤ 0.001) varied with all three factors i.e. season, location and tissue type. Leaves supported the highest diversity across all the seasons and locations. In conclusion, all the three factors together determined the structure of endophytic mycobiota assemblage of T. grandis.

Hydrogen bonding patterns in different acrylamide–water clusters: microsolvation probed by micro Raman spectroscopy and DFT calculations

We report in this study on the hydrogen bonding patterns between acrylamide (Acr) and water (W) as a H-donor. Hydrogen bonds between Acr and water molecules and among different water molecules significantly influence the spectral features. Raman spectra of neat Acr and its mixtures with water were recorded in the region, 1800–400 cm−1. A careful analysis of the spectra reveals that upon dilution, the additional peaks are observed at 831 and 1124 cm−1, ∼10 and ∼18 cm−1 away from the main bands at ∼842 and ∼1142 cm−1, respectively, which were attributed to the hydrogen bonding of Acr with water. The new band at ∼1083 cm−1 clearly reveals a nice example of the increment on the degree of hydrogen bonding in terms of multiple hydrogen bonded molecules. The temperature dependent Raman spectra of Acr at nine different temperatures were also recorded, and a significant change in spectral features observed at ∼373 K is attributed to crystal → liquid transition. A new peak at 1620 cm−1 appears to be due to a change in the symmetry of self associated Acr (dimer and trimer) molecules at 373 K. DFT calculations were performed using B3LYP/6-311++G(d,p) to obtain the ground state optimized geometries of neat, self associated dimeric and trimeric forms, and hydrogen bonded complexes in gas phase. The DFT computations were also performed on various (Acr + Wn, n = 1–15) clusters in order to explore the microsolvation. A broad configuration search was performed to identify the lowest energy clusters of Acr with varying number of water molecules. The structures of the clusters are analyzed in terms of the hydrogen bonding network established among the water molecules and between Acr and water molecules. Overall the present study gives a clue regarding the stabilization of the Acr molecule in a large cluster of water molecules.

Epigenetic Activation of Antibacterial Property of an Endophytic Streptomyces coelicolor Strain AZRA 37 and Identification of the Induced Protein Using MALDI TOF MS/MS

The endophytic Streptomyces coelicolor strain AZRA 37 was isolated from the surface sterilized root of Azadirachta indica A. Juss., commonly known as neem plant in India. Since only a few reports are available regarding epigenetic modulations of microbial entities, S. coelicolor was treated with different concentrations of 5-azacytidine for this purpose and evaluated for its antibacterial potential against five human pathogenic bacteria (Aeromonas hydrophila IMS/GN11, Enterococcus faecalis IMS/GN7, Salmonella typhi MTCC 3216, Shigella flexneri ATCC 12022 and Staphylococcus aureus ATCC 25923). The crude extract obtained from cultures treated with 25 μM concentration of 5-azacytidine, was found effective against all five pathogenic bacteria tested while the untreated control was only active against 3 pathogenic bacteria. HPLC analysis of crude compounds from treated cultures showed a greater number of compounds than that of the control. Extraction of whole cell protein and its SDS PAGE analysis showed an additional major protein band in 25 μM 5-azacytidine treated culture and MALDI TOF MS/MS analysis revealed that this protein belongs to the porin family.

Raman Spectroscopic Study on Alkyl Chain Conformation in 1‐Butyl‐3‐methylimidazolium Ionic Liquids and their Aqueous Mixtures

Ionic liquids of 1-butyl-3-methylimidazolium ([BMIM]) cation with different anions (Cl- , Br- , I- , and BF4- ), and their aqueous mixtures were investigated by using Raman spectroscopy and dispersion-included density functional theory (DFT). The characteristic Raman bands at 600 and 624 cm-1 for two isomers of the butyl chain in the imidazolium cation showed significant changes in intensity for different anions as well as in aqueous solutions. The area ratio of these two bands followed the order I- >Br- >Cl- >BF4- (in terms of the anion X in [BMIM]X), indicating that the butyl chain of [BMIM]I tends to adopt the trans conformation. The butyl chain was found to adopt the gauche conformation upon dilution, irrespective of the anion type. The Raman bands in the butyl C-H stretch region for [BMIM]X (X=Cl- , Br- , and I- ) blueshifted significantly with the increase in the water concentration, whereas that for [BMIM]BF4 changed very little upon dilution. The blueshift in the C-H stretch region upon dilution also followed the order: [BMIM]I>[BMIM]Br>[BMIM]Cl>[BMIM]BF4 , the same order as the above trans conformation preference of the butyl chain in pure imidazolium ionic liquids, which suggested that the cation-anion interaction plays a role in determining the conformation of the chain.

Study of hydration of sarcosine, formation of its zwitterion and their different oligomers in aqueous media: a Raman spectroscopic and theoretical study.

Raman spectra of the biologically important molecule sarcosine (SAR) (C3H7NO2) were studied experimentally in aqueous solution at different concentrations. These spectra were also calculated theoretically using density functional theory (DFT) at the B3LYP/6-311++G(d,p) level. Further, all the observed normal modes were assigned through potential energy distribution (PED). Geometry optimization of SAR produced its three conformers with slightly different energies. The lowest energy conformer of SAR was selected for a systematic solvation study wherein different numbers of water molecules (nW, n=1-9) were placed near it. In the SAR-9W complex, the SAR molecule is located almost at the center of the cage of 9 water molecules. Geometries of different oligomers of SAR (dimer, trimer, tetramer and pentamer) were also optimized in aqueous media taking the input structures from crystallographic data and using the polarizable continuum (PCM). Proton transfer required for the formation of the zwitterionic form of SAR was found to occur when the number of water molecules in the first hydration shell was six or more.