Department of Chemistry
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Item Conformational and environmental determinants of RNA solvation dynamics: roles of intrinsic flexibility, allostery, and protein binding(2025) Chakraborty, AmritaSolvation dynamics play a central role in shaping nucleic acid structure, flexibility, and recognition, yet their molecular origins remain poorly understood for RNA, whose diverse architectures and intrinsic conformational plasticity far exceed those of DNA. Here, we present the atomistic, microsecond-scale computational dissection of solvation dynamics in two structurally homologous but functionally distinct viral RNAs—BIV TAR and HIV-2 TAR—in both apo and peptide-bound states mimicking the salt concentration of experimental time-resolved fluorescent spectroscopic measurement. By combining high-temporal-resolution solvation time correlation functions with detailed energy decomposition analyses, we uncover how water, ions, and RNA motions cooperatively shape relaxation across ultrafast to nanosecond timescales. Our results reveal that, unlike DNA, where slow components primarily reflect long-lived hydration and ion condensation, RNA can generate slow solvation decay either through long-lived hydration or through its own internal conformational fluctuations, such as involving spontaneous base-flipping events. Peptide binding modulates this conformational landscape in strikingly system-specific ways: BIV TAR RNA undergoes classical fluctuation quenching, where TAT binding suppresses RNA motions and shifts relaxation toward solvent–RNA compensation, whereas HIV-2 TAR RNA exhibits a non-classical redistribution of solvent–ion–peptide correlations stemming from its weaker and more dynamic binding interface with TAT. The dominant slow decay in HIV-2 apo TAR maps directly onto an allosteric communication channel previously identified from structural analyses, demonstrating that solvation responses can sensitively report on RNA allostery. Together, this study bridges the experimental observations of time resolved fluorescence spectroscopy with mechanistic molecular insight, establishes solvation dynamics as a powerful probe of RNA conformational energetics, and highlights how subtle differences in RNA–protein recognition can imprint distinct signatures on hydration and ion reorganization.Item Matrix-isolation IR spectroscopy and quantum chemical characterisation of SOCl2 and [SOCl2 single bondHCl] clusters(Elsevier, 2025-11) Chakraborty, Amrita; Chakraborty, ShamikThe IR spectra of thionyl chloride (SOCl2) are reported for the first time under matrix-isolation conditions in argon and nitrogen matrices, focusing on symmetric and antisymmetric stretching, and stretching modes. Spontaneous hydrolysis of SOCl2 to SO2 and HCl is observed, as evidenced by distinct IR peaks. Two conformers of and three conformers of [ ] have been identified on their respective potential energy surfaces. The formation of two dimer conformers is confirmed by characteristic SOCl2 modes, while the formation of three [ ] clusters is confirmed by red-shifts in the HCl stretching frequency mode.Item Mapping allosteric rewiring in viral RNA: sequence-encoded control of protein binding mechanisms(2025) Chakraborty, AmritaRNA recognition by proteins is governed not only by static structure but also by allostery encoded within non-local dynamic motifs. In this study, we systematically identify allosteric communication hubs in RNA and map multiple residue-connected pathways, revealing how these networks are rewired upon mutation and protein binding. To capture these effects under physiological salt conditions, we performed tens of microseconds of atomistic and steered molecular dynamics simulations and computed binding free energies for Tat–TAR complexes across three immunodeficiency virus variants, BIV, HIV-1, and HIV-2. Allosterically coupled sites were identified using contact-based principal component analysis, and communication pathways were traced through an extended graph-network algorithm—the first such application to RNA systems. Two distant motifs—the bulge and the apical loop—emerge as allosteric switches and information hubs: the bulge engages Tat, while the loop interacts with another protein partner, CycT1, both essential for transcriptional activation and antiviral targeting. We find that HIV-2 TAR, with strong loop–bulge coupling and high self-integrity, favour conformational selection and exhibits lower Tat-binding affinity. In contrast, a single C24 insertion in HIV-1 TAR reconfigures communication pathways, enabling an induced-fit mechanism with enhanced affinity. The study not only elucidates an allosteric rewiring between the loop and bulge but also highlights how this communication is dynamically reconfigured upon protein binding. Tat association at the bulge reorganizes and reorients loop residues, thereby promoting the subsequent recruitment of CycT1. This work overall underscores how sequence (even a single mutation) encoded RNA allostery can modulate not only a protein’s binding mechanism and affinity but also influence downstream molecular events within transcriptional signalling cascades.Item Organic components modulate the morphology of respirable aerovirology-relevant aerosols(2026-01) Chakraborty, AmritaAirborne transmission of pathogens occurs via aerosol particles, whose morphology provides insights into the microenvironments that pathogens experience. Aerosol morphology includes particle size, shape, phase state, and chemical homogeneity, yet systematic studies remain limited. Here, we characterized model bioaerosol morphologies generated from (1) NaCl–organic two-component mixtures, (2) common cell culture media, and (3) artificial respiratory fluids. Particles were collected using a virtual impactor and Andersen cascade impactor and analyzed by scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDX). Results show that organic components modulate the morphology: dipalmitoylphosphatidylcholine (DPPC) promotes organic-inorganic phase separation while proteins prohibit formation of large crystals and leads to better mixing among components. At 30% RH with a drying period of 10 seconds, most aerosols appeared desiccated, though NaCl-glucose, DMEM-complete-media and artificial saliva with mucin remained semi-solid or gel-like. Among all formulations examined EMEM-complete-media and artificial saliva (non mucin) show a size-dependent morphology. Our study demonstrates how chemical composition and size alters surrogate bioaerosol phase (semi-solid or solid) and morphology and provides new insights into the microenvironment of aerosol particles for aerovirology investigations.Item Investigation of the molecular level interaction in [ch3oh−ch2x2] Complexes (x=I, br, and cl) using matrix-isolation ir spectroscopy(Wiley, 2025-01) Chakraborty, Amrita; Chakraborty, ShamikThe mathematical equation (X=Cl, Br, and I) complexes have been studied to understand the tendency towards the formation of hydrogen bonds and halogen bonds. Three different types of interactions viz., C–Xmathematical equation O, C-Hmathematical equation O, and O-Hmathematical equation X, are possible between the mathematical equation and mathematical equation . Experiments have been carried out in low temperature mathematical equation matrix using Fourier Transform Infrared spectroscopy. Electronic structure calculations have been performed to identify the possible binding motifs between mathematical equation and mathematical equation . Formation of more than one complex has been confirmed in mathematical equation (X=Br and I) mixture, using the experimental and simulated IR spectra, whereas only one type of complex is found in mathematical equation mixture. Energy decomposition analysis, quantum theory of atoms in molecules, and non-covalent interaction analysis have been performed to understand the nature of interaction and the driving force for complexation under experimental conditions.Item Investigation of [CH2I2–R2S] complexes (R = –H, –CH3) in cryomatrix: Propensity towards C–I⋯S halogen bond and C–H⋯S hydrogen bond interaction(Elsevier, 2025-12) Chakraborty, Amrita; Chakraborty, ShamikThe volatile organic iodine compound (Image 1) and volatile bivalent sulphur compounds, such as, Image 2, Image 3, are trace gases present with high concentration in the coastal area and are important constituents for the chemical processes in the area of atmospheric science. The Image 4 is one of the iodine precursors in the atmosphere, and Image 5 and Image 6 play a major role in the sulphur cycle. Depending on the nature of the Lewis bases, the type of interactions between the constituents may alter, which would influence the final product in a chemical reaction, nucleation process, and radiative forcing. The key objective of this work is to understand the plausible interaction between Image 7 and sulphur-containing Lewis bases (Image 8, Image 9), and to identify the propensity towards the formation of hydrogen bond and halogen bond interaction at the molecular level using matrix-isolation FTIR spectroscopy. Electronic structure calculations have been performed in the ground electronic state to predict the possible structures and stability of the clusters. The thermodynamic properties of the dimers have been evaluated along with their higher-order clusters to understand the possibility of forming such complexes in the atmosphere.Item IR spectra of CH2I2 in Ar and N2 cryomatrices: Evidence of unusual band splitting in N2 matrix(Springer, 2022-08) Chakraborty, Amrita; Chakraborty, ShamikMatrix isolation IR spectra of in matrix are analysed using IR spectra obtained in the Ar matrix, quantum chemical calculations, and molecular point group symmetry to determine the origin of the unusual splitting observed in the antisymmetric stretching (), rocking (), wagging (), and antisymmetric stretching () modes of only in matrix and not in Ar matrix. The , , , and vibrational modes belong to either or irreducible representations under point group symmetry. IR spectra in matrix is reported for the first time. IR spectra recorded in Ar matrix are consistent with previous reports. Electronic structure calculations have been performed to obtain simulated IR spectra of with and point group symmetries, conformers, [-], and [-]. IR spectra obtained in Ar and matrices originate from , , and splitting of IR peaks in matrix. Splitting of the IR peaks of in solid state is described by Davydov splitting or factor group splitting. The observed splitting of IR peaks in matrix is due to the lowering of symmetry of from to one of its sub groups due to the perturbation of the rigid matrix that possess quadrupole moment.Item IR spectra of in Ar and cryomatrices: Evidence of unusual band splitting in matrix(Elsevier, 2022-08) Chakraborty, Amrita; Chakraborty, ShamikMatrix isolation IR spectra of in matrix are analysed using IR spectra obtained in the Ar matrix, quantum chemical calculations, and molecular point group symmetry to determine the origin of the unusual splitting observed in the antisymmetric stretching (), rocking (), wagging (), and antisymmetric stretching () modes of only in matrix and not in Ar matrix. The , , , and vibrational modes belong to either or irreducible representations under point group symmetry. IR spectra in matrix is reported for the first time. IR spectra recorded in Ar matrix are consistent with previous reports. Electronic structure calculations have been performed to obtain simulated IR spectra of with and point group symmetries, conformers, [-], and [-]. IR spectra obtained in Ar and matrices originate from , , and splitting of IR peaks in matrix. Splitting of the IR peaks of in solid state is described by Davydov splitting or factor group splitting. The observed splitting of IR peaks in matrix is due to the lowering of symmetry of from to one of its sub groups due to the perturbation of the rigid matrix that possess quadrupole moment.Item Investigation of [CHCl3-CH3OH] complex using matrix-isolation IR spectroscopy and quantum chemical calculation: Evidence of hydrogen- and halogen-bonding interaction(Elsevier, 2022-03) Chakraborty, Amrita; Chakraborty, ShamikMixture of CHCl3-CH3OH is a popular non-aqueous solvent mixture that exhibits strong synergistic solvation. The specific interaction between the CHCl3 and CH3OH is investigated using 1:1 complex in N2 matrix along with electronic structure calculation. Three different type of interactions are possible between CHCl3 and CH3OH at the molecular level: C-HO hydrogen bond, O-HCl hydrogen bond, and C-ClO halogen bond. One C-HO hydrogen bond minimum, two O-HCl hydrogen bond minima, and one C-ClO halogen bond minimum are obtained on the [CHCl3-CH3OH] dimer potential energy surface. Formation of C-HO hydrogen bonded and C-ClO halogen bonded 1:1 complex of [CHCl3-CH3OH] in N2 matrix is confirmed using experimental and simulated IR spectra. The outcome of the current work would help to explain the specific interactions present in CHCl3 and CH3OH binary solvent mixture and to estimate the responses of such non-aqueous solvent mixture.Item Hydrogen bond properties of Se in [ROH–Se(CH3)2] complexes (R = H, CH3, C2H5): matrix-isolation infrared spectroscopy and theoretical calculations(RSC, 2023-03) Chakraborty, Amrita; Chakraborty, ShamikSe is now considered as a potential centre for hydrogen bond interactions. The hydrogen bond acceptor ability of Se has been investigated in [ROH–Se(CH3)2] complexes (R = H, CH3, and C2H5) using matrix-isolation infrared spectroscopy and electronic structure calculations. The first impression of the IR spectra of the hydrogen bond complexes of [ROH–Se(CH3)2] in N2 and Ar matrices is presented here. Moreover, no spectroscopic data are available for the [HOH–Se(CH3)2] complex. Vibrational spectra in the OH stretching region indicate the formation of the [ROH–Se(CH3)2] complex under the matrix-isolation conditions. Comparison of the experimental spectra with the simulated vibrational frequencies at different levels of theory confirms the formation of the 1[thin space (1/6-em)]:[thin space (1/6-em)]1 cluster of [ROH–Se(CH3)2] stabilised by O–H⋯Se hydrogen bond interactions. Multiple conformers of the [CH3OH–Se(CH3)2] complex having marginally different stabilisation energies have been predicted from electronic structure calculations and signatures of the same have been observed under the cold conditions of matrix isolation. Conformer specific assignment of the 1[thin space (1/6-em)]:[thin space (1/6-em)]1 cluster of [C2H5OH–Se(CH3)2] (anti and gauche forms) has been carried out in both the matrices. Concentration dependent experiments indicate the formation of higher order clusters and/or mixed clusters along with the formation of a 1[thin space (1/6-em)]:[thin space (1/6-em)]1 cluster for CH3OH and C2H5OH. The nature of the selenium centred hydrogen bond has been delineated using AIM, NBO and energy decomposition analysis. A comparison of similar complexes of H2O, CH3OH, and C2H5OH with O, S and Se indicates that Se is not far away in hydrogen bond acceptor ability compared to O and S.