Joydeep Chowdhury

Concentration-dependent surface-enhanced resonance Raman scattering of a porphyrin derivative adsorbed on colloidal silver particles

Surface-enhanced Raman spectra (SERS) of 5,10,15,20-tetrakis(1-decylpyridium-4-yl)-21H,23H-porphintetrabromide or Por 10 (H(2)Tdpyp) adsorbed on silver hydrosols are compared with the FTIR and resonance Raman spectrum (RRS) in the bulk and in solution. Comparative analysis of the RR and the FTIR spectra indicate that the molecule, in its free state, has D(2h) symmetry rather than C(2v). The SERS spectra, obtained on adsorption of this molecule on borohydride-reduced silver sol, indicate the formation of silver porphyrin. With the change in the adsorbate concentration, the SERS shows that the molecule changes its orientation on the colloidal silver surface. The appearance of longer wavelength band in the electronic absorption spectra of the sol has been attributed to the coagulation of colloidal silver particles in the sol. The long wavelength band is found to be red-shifted with the decrease in adsorbate concentration. The excitation profile study indicates that the resonance of the Raman excitation radiation with the original sol band is more important than that with the new aggregation band for the SERS activity. This indicates a large contribution of electromagnetic effect to surface enhancement.

Conformational preferences of ethyl propionate molecule: Raman, temperature dependent FTIR spectroscopic study aided by ab initio quantum chemical and Car-Parrinello molecular dynamics simulation studies.

The conformational preferences of the industrially significant ethyl propionate (EP) molecule have been investigated from the Raman and FTIR spectra, aided by ab initio and Car-Parrinello molecular dynamics (CPMD) simulation studies. The vibrational signatures of various rotameric forms of the EP molecule have been assigned for the first time from the potential energy distributions (PEDs). The critical analyses of the vibrational signatures reveal the coexistences of the Trans-Trans (TT), Trans-Antigauche (TG(-)) [Trans-Gauche (TG(+))], Antigauche-Trans (G(-)T) [Gauche-Trans (G(+)T)], Antigauche-Antigauche (G(-)G(-)) [Gauche-Gauche (G(+)G(+))], and Gauche-Antigauche (G(+)G(-)) [Antigauche-Gauche (G(-)G(+))] forms of the EP molecule at room and at high temperatures. However, at low temperature (ca. 70 °C), the TT and TG(-) forms of the EP molecule is estimated to be preponderant. The Car-Parrinello molecular dynamics simulation studies of the EP molecule estimated at high, room, and low temperatures are also in harmony with our conjecture as suggested from the vibrational analyses. The ab intio molecular dynamics simulations are observed to be a useful tool for the conformational analyses of the molecule.

A two-component hydrogelator from citrazinic acid and melamine: synthesis, intriguing role of reaction parameters and iodine adsorption study

Herein, we have implemented an intimate grinding–mixing protocol (GMP) for the synthesis of a new hydrogelator from citrazinic acid and melamine. Sonication, just for a few seconds, of the ground mixture in a suitable solvent/mixed-solvent system finally results in the formation of a gel matrix. Citrazinic acid is decorated with ureidopyrimidone functionalities and melamine is enriched with aminopyridine functionalities. Therefore, the necessary non-covalent interactions (like hydrogen bonding and π–π stacking) become part-and-parcel of this reaction, bringing a nanofibrous gel material into existence. A thorough and complete solvent-dependent gelation investigation suggests that water must be present as the sole solvent or one of the members of other mixed-solvent systems to successfully result in gel formation. The gel shows an entangled network morphology. Different micro-analytical studies (FTIR, powder XRD, FESEM, TEM, rheology, etc.) have been conducted for complete characterization of the gel sample. The gel also exhibits stimuli-responsive behaviour towards different interfering chemical parameters like pH, selective anions, etc. Again, it is worth mentioning that here, GMP plays a key role in strongly initiating and improvising solid-state self-assembly. Different non-covalent interactions afford a suitable hydrogen-bonded motif which presumably propagates upon activation in solution phase after mild sonication, favouring the spontaneous formation of fibrous architectures. It is also noticed that without grinding, the solid-state interactions are jeopardized and only a partial gel structure prevails. Finally, the available porosity in the gel framework and the enriched π-electron density within the structure make the gel a suitable host for adsorption of guest molecules. This information provoked us to study the reversible adsorption–desorption equilibrium of molecular iodine within the dried-gel matrix. The guest iodine entrapment into the host occurs both from the solution and also from gas-phase iodine. The complete analysis suggests that our material presents a high storage capacity for this halogen species. Therefore, the study prescribes that the synthesized hydrogel material could be a suitable candidate for application in synthetic organic chemistry and would find an avenue to solve other environmental issues also.

How the Charge Transfer (CT) Contributions Influence the SERS Spectra of Molecules? A Retrospective from the View of Albrecht's “A” and Herzberg-Teller Contributions

Abstract The role of charge transfer (CT) contribution to the surface-enhanced Raman scattering (SERS) effect from the view of Albrechts “A” and Herzberg-Teller (HT) contributions is presented. The basic understanding of Albrechts “A,” “B,” and “C” terms and the HT selection rule are explained to understand the SERS-CT mechanism. The Albrechts “A” and HT selection rule are then applied to wide varieties of organic molecules to test their relevance.

Vibrational analysis of the conformers and understanding the genesis of the internal rotational barriers of Isobutyl Cyanide molecule

Molecular structure and conformational properties of Isobutyl Cyanide (IBCN) have been studied by quantum chemical methods. The quantum chemical methods predict the existence of both the Trans-Gauche (TG) and Gauche-Gauche (GG) rotameric forms of the IBCN molecule. Fresh vibrational assignments corresponding to each of the 39 normal modes are proposed for both the TG and GG rotameric forms of the molecule. The origin of the internal rotational barrier of the TG form of the molecule has been studied by the relaxation effects and with the aid of nuclear virial and natural bond orbital (NBO) analyses technique. For the barrier to internal rotation of the methyl CH(3) (I)/CH(3) (II) groups of the TG form of the IBCN molecule; the combined relaxations of the C(2)-C(3)/C(2)-C(4) bond lengths and H(10)-C(3)-H(11)/C(2)-C(4)-H(13) angles together play a significant role.

Targeting G-quadruplex DNA and B-DNA with a natural alkaloid: a comparative spectroscopic study

The present research compared the binding mechanisms of natural alkaloid harmine (HR) with two structurally different biologically important DNA species, human telomeric 22 G-quadruplex DNA (GQ-DNA) and B-DNA using various steady state and time-resolved spectroscopic techniques. Our study shows that for both DNA species HR has appreciable ground state interaction with comparable binding strengths. When HR binds, GQ-DNA which initially remained as mixed-hybrid structure converted to parallel types whereas the B-DNA structure perturbed through intercalation. HR displayed modest selectivity for the quadruplex over duplex B-DNA and binds in grooves and/or loops over external end stacking with quadruplex instead of intercalation with B-DNA. Switching of stabilization from moderate to strong occurred while HR binds with GQ-DNA and B-DNA respectively. The difference in the dynamics of HR in with both DNAs has been described well by the wobbling-in-cone model from the time-resolved anisotropy data. Our time-resolved results interpreted the dynamics of HR in both DNA environments suggesting favourable loop and/or groove binding of HR with GQ-DNA over partial end-stacking and intercalation mode of binding with B-DNA. Steady state anisotropy measurements and molecular docking further confirmed our conclusions regarding binding mechanisms. The present study could be highly useful in less toxic targeted gene therapy.

Excited Electronic States and Raman Spectra of 2-Benzoylpyridine

Raman excitation profiles of several normal modes of 2-benzoylpyridine were measured, and the structural changes encountered on excitations, excited state symmetries, and vibronic couplings among various excited electronic states of the molecule were investigated. Vibrational spectroscopic studies of the molecule were done in detail, and critical investigation on the electronic spectra of the molecule was also carried out. It is shown that the experimentally allowed transitions, corresponding to the band around 262 and 238 nm, occur to the excited states, where the major geometry changes involve both ring CC/CN and CO stretching vibrations. An excited state lying around 185 nm above the ground state was also found to play an important role in the scattering process. All necessary and valuable quantum chemical calculations accompany the presented spectral studies.

Resonance Raman Spectroscopy: Principles and Applications

In this chapter, the basic principle, instrumentation, and the analytical potential of resonance Raman spectroscopy (RRS) have been highlighted. The basic principles of Raman and RRS are discussed in the light of Albrechts “A” and “B” terms. Advancement in Raman instrumentation, after the invention of lasers, is discussed with special emphasis on the source and the detector systems. Analytical applications of RR in agriculture, life sciences, art, archaeology, and forensics are conversed. Recent applications of RRS in carbon nanotube research, exploring the effect of solvent polarity, isomerization dynamics of organic molecules and understanding the contributions of different electronic states of aromatic closed ring compounds to Raman scattering are highlighted. Recent studies on the applications of RRS to understand the excited electronic states of metal–ligand complexes and charge transfer mechanism in halide-substituted hybrid perovskite solar cells are also discussed.In this chapter, the basic principle, instrumentation, and the analytical potential of resonance Raman spectroscopy (RRS) have been highlighted. The basic principles of Raman and RRS are discussed in the light of Albrechts “A” and “B” terms. Advancement in Raman instrumentation, after the invention of lasers, is discussed with special emphasis on the source and the detector systems. Analytical applications of RR in agriculture, life sciences, art, archaeology, and forensics are conversed. Recent applications of RRS in carbon nanotube research, exploring the effect of solvent polarity, isomerization dynamics of organic molecules and understanding the contributions of different electronic states of aromatic closed ring compounds to Raman scattering are highlighted. Recent studies on the applications of RRS to understand the excited electronic states of metal–ligand complexes and charge transfer mechanism in halide-substituted hybrid perovskite solar cells are also discussed.

Sensing of Different Human Telomeric G-Quadruplex DNA Topologies by Natural Alkaloid Allocryptopine Using Spectroscopic Techniques

This article describes how a natural alkaloid allocryptopine (ALL) is able to differentiate two forms of biologically relevant human telomeric (htel22) G-quadruplex DNAs (GQ-DNA) depending on the presence of K+ and Na+ ions by steady-state and time-resolved spectroscopic techniques. For both interactions, predominant involvements of static-type quenching mechanism with the negligible influence of dynamic collision are established by UV-vis absorption and fluorescence emission study, which is further supported by fluorescence lifetime measurements. ALL exhibits appreciable affinity toward both GQ-DNAs. Both the mixed-hybrid (3 + 1) quadruplex structures in K+ ions and the basket-type antiparallel quadruplex structure under Na+ condition are converted to parallel types in the presence of ALL. Fluorescence intercalator displacement assay experiment revealed modest selectivity of ALL to both quadruplexes over duplex DNA along with higher selectivity for antiparallel types among the two quadruplexes via groove and/or loop binding, which is distinct from the conventional π-stacking of the ligands on external G-quartets. ALL stabilized both GQ-DNA topologies moderately. The differences in the dynamics of ALL within both DNA environments have been demonstrated vividly by time-resolved anisotropy measurements using the wobbling-in-cone model. These results suggest groove binding with antiparallel G-quartet with high affinity and moderate loop binding with mixed-hybrid G-quartet accompanied by the partial end stacking additionally in both of the cases. Our conclusions are further supported by steady-state anisotropy measurements and molecular docking. The present investigation can be used in the development of a biocompatible antitumour/anticancer agent targeting particular GQ-DNA conformation.

Physics behind the Barrier to Internal Rotation of an Acetyl Chloride Molecule: A Combined Approach from Density Functional Theory, Car–Parrinello Molecular Dynamics, and Time-Resolved Wavelet Transform Theory

The physics behind the barriers to internal rotation of acetyl chloride (AC) molecule has been reported. The AC molecule closely resembles the molecular structure of acetaldehyde; the only subtle difference is the presence of a heavy chlorine atom in place of the hydrogen atom of the aldehyde group for the latter. This paper aims to study the effect of substitution of the heavy chlorine atom on the barrier energetics of the AC molecule. The reason behind the barrier for the AC molecule has been estimated for the first time from the unified approach using barrier energetics, natural bond orbital, nuclear virial, and relaxation analyses using density functional theory, Car–Parrinello molecular dynamics, and wavelet transform theory. Complete analyses reveal the concomitant relaxations of both the in-plane Cmethyl–C1 and Cmethyl–H4 bonds toward understanding the origin of the barrier due to internal rotation for the AC molecule. The large negative value of “V6” further suggests that both the abovementioned degrees of freedom are coupled with the −CH3 torsional vibration of the molecule. The coupling matrix (H12) element has also been estimated. Time-resolved band stretching frequencies of Cmethyl–C1 and C1–Cl3 bonds of the AC molecule, as obtained from wavelet transformation analysis, primarily preclude the possibility of coupling between the C1–Cl3 bond and the torsional motion associated with the methyl group of the molecule.