Browsing by Author "Chakraborty, Amrita"

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Atmospherically relevant halogen- and hydrogen- bond complex [CCl4 single bond(H2Y)n] with Y = O and S, n 4: A computational study on Rayleigh scattering properties
(Elsevier, 2023-11) Chakraborty, Amrita; Chakraborty, Shamik
In troposphere, CCl4 may interact with volatile compounds that may finally contribute to the aerosol formation or atmospheric nucleation. Herein, first solvation shell of CCl4 with (H2O)n and (H2S)n is investigated. The Csingle bondClO and Csingle bondClS types of halogen bond and Osingle bondHCl and Ssingle bondHCl types of hydrogen bond have been considered. Molecular structure of the complexes have been optimised at the MP2/aug-cc-pVTZ level and the stabilisation energies are calculated at the CCSD(T)/aug-cc-pVTZ level. Halogen bond complexes of [CCl4 single bond(H2O)n] are more stable compared to the hydrogen bond complexes. Stability of halogen and hydrogen bond complexes of [CCl4 single bond(H2S)n] are comparable. The Rayleigh scattering intensity of these complexes have been investigated for the first time. Rayleigh scattering intensity increases with the number of H2O and H2S molecules in the complexes. The Rayleigh scattering intensity of the halogen bond complexes are higher compared to the hydrogen bond complexes.
Competition between the hydrogen bond and the halogen bond in a [CH3OH–CCl4] complex: a matrix isolation IR spectroscopy and computational study
(RSC, 2020) Chakraborty, Shamik; Chakraborty, Amrita
Methanol (CH3OH) is the simplest alcohol and carbon tetrachloride (CCl4) is widely used as a solvent in the chemical industry. CH3OH and CCl4 are both important volatile substances in the atmosphere and CCl4 is an important precursor for atmospheric ozone depletion. Moreover, mixtures of CH3OH and CCl4 are an important class of non-aqueous mixtures as they exhibit a large deviation from Raoult's law. The specific interaction between CH3OH and CCl4 is not yet investigated experimentally. The interaction between CH3OH and CCl4 at the molecular level can be twofold: hydrogen bond (O–H⋯Cl) and halogen bond (C–Cl⋯O) interaction. One halogen bonded minimum and two hydrogen bonded minima are identified in the dimer potential energy surface. Herein, the 1 : 1 complex of [CH3OH–CCl4] has been characterised using matrix-isolation infrared spectroscopy and electronic structure calculations to investigate the competition between hydrogen bonded and halogen bonded complexes. Vibrational spectra have been monitored in the C–Cl, C–O, and O–H stretching regions. The exclusive formation of halogen bonded 1 : 1 complexes in argon and nitrogen matrices is confirmed by a combination of experimental and simulated vibrational frequency, stabilisation energy, energy decomposition analysis, and natural bond orbital and atoms-in-molecules analyses. This investigation helps to understand the specific interactions in the [CH3OH–CCl4] mixture and also the possibilities of formation of halogen bonded atmospheric complexes that may influence the atmospheric chemical activities, and enhance aerosol formation and deposition of CCl4.
Conformational and environmental determinants of RNA solvation dynamics: roles of intrinsic flexibility, allostery, and protein binding
(2025) Chakraborty, Amrita
Solvation 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.
Effect of ionic charge on O H⋯Se hydrogen bond: A computational study
(Elsiever, 2017-02-15) Chakraborty, Shamik; Chakraborty, Amrita
Complexes between para-substituted cationic phenol and SeH2 have been investigated in electronic ground state at the B3LYP, B3PW91, and ωB97xD levels of theory using 6-311++G(3df,3pd) basis set. Various electron-donating and withdrawing substituents (NH2, OH, CH3, H, F, Cl, CN, and NO2) are used to characterize electronic substituent effect on intermolecular +OH⋯Se hydrogen bond. Electron withdrawing substituent increases hydrogen bond stabilization energy and red shift in OH stretching frequency. Introduction of a positive charge transforms weak hydrogen bond of neutral OH⋯Se type into a strong hydrogen bond. Complexation induced changes on various hydrogen bond parameters, such as, stabilization energy, change in OH bond length, change in OH stretching frequency, extent of charge transfer from hydrogen bond acceptor to donor, hydrogen bond orders, electron density at the hydrogen bond critical point exhibit conventional electronic substitution effect. Stabilization energy of +OH⋯Y hydrogen bond are similar in the complexes between cationic phenol and SH2/SeH2, whereas it is almost twice with OH2 in case of +OH⋯Y hydrogen bond.
Electronic substituent effect on Se-H⋯N hydrogen bond: A computational study of para-substituted pyridine-SeH2 complexes
(Elsiever, 2019) Chakraborty, Shamik; Chakraborty, Amrita
Complexes between para-substituted pyridine and SeH2 have been investigated at the MP2/aug-cc-pVTZ level. Various electron donating and withdrawing substituents (-NH2, -OH, -CH3, -H, -F, -Cl, -CN, and -NO2) are chosen in order to characterize their influence on Se-H⋯N intermolecular hydrogen-bonding interaction. The electron donating substituents lead to an increase of the stabilization energy along with elongation in the Se-H bond length and red-shift in Se-H stretching frequency. Conventional electronic substitution effect has been observed on various hydrogen-bond parameters, such as, stabilization energy, change in Se-H bond length and stretching frequency, charge transfer, bond order, electron density at hydrogen-bond critical point.
Ethanol monomer revisited: Thermal isomerisation between anti and gauche conformers in Ar and N2 matrix
(Elsiever, 2020-09-01) Chakraborty, Shamik; Chakraborty, Amrita
The anti-gauche conformational distribution of ethanol has been investigated using the and symmetric stretching infrared spectra in argon and nitrogen matrix. The dipole moment of the gauche conformer is higher compared to the anti conformer. The relative population of the anti and gauche conformer of ethanol depends on the rare gas mixture in the gas phase and also in the matrix after thermal cyclisation. In the gas phase, the anti conformer is more populated in nitrogen mixture whereas the gauche conformer is more populated in the argon mixture. After thermal cyclisation in the matrix, the anti conformer isomerise to the gauche conformer in nitrogen matrix and reverse happens in the argon matrix. Thermal cyclisation at 30 K in nitrogen matrix leads to the splitting of the gauche states that is probed by monitoring symmetric stretching frequency mode.
Experimental and theoretical investigation of ground state intramolecular proton transfer (GSIPT) in salicylideneaniline Schiff base derivatives in polar protic medium
(Elsiever, 2020-01-15) Chakraborty, Shamik; Chakraborty, Amrita
Ground state intramolecular proton transfer process has been comprehensively investigated in three salicylideneaniline Schiff base derivatives (SB1, SB2, and SB3) using experimental and theoretical methods. It has been confirmed that all the three Schiff base molecules in the ground electronic state exist in the enol form in non-polar and polar aprotic solvents. Keto form is being populated by the polar protic solvent through ground state intramolecular proton transfer (GSIPT) process. Ground state equilibrium between the enol and keto tautomers for SB1 and SB3 is mainly governed by the proton donating ability of the solvent. Ground state equilibria between the enol and keto tautomers of SB2 which is a positional isomer of SB3 is governed by the polarity and proton donating ability of the solvents. Excited state intramolecular proton transfer (ESIPT) process is also evidenced in all the three Schiff base molecules. Theoretical calculations at the B3LYP/cc-pVDZ level in the gas phase and in different solvents using polarisable continuum model (PCM) have failed to establish the GSIPT process. Microsolvation of individual enol and keto conformers has been investigated considering upto three solvent molecules. The energetics of the individual conformers together with the corresponding transition state have been calculated. It has been confirmed that the keto conformer is more stable compared to the enol conformer in microsolvated cluster of three methanol molecules. Lowering of activation energy for the enol to keto tautomerisation in the presence of methanol also supports the experimental observation for GSIPT process. TDDFT/B3LYP/cc-pVDZ single point calculations for microsolvated clusters of enol and keto form of the Schiff base molecules exhibit an excellent agreement with the experimentally obtained absorption spectra. Difference in spectral nature of the Schiff base molecules has been explained using natural bond orbital (NBO) analysis. Quantum theory of atoms in molecules (QTAIM) has also been utilised to understand the GSIPT process in detail.
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, Shamik
Se 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.
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, Shamik
The 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.
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, Shamik
Mixture 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.
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, Shamik
The 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.
IR spectra of CH2I2 in Ar and N2 cryomatrices: Evidence of unusual band splitting in N2 matrix
(Springer, 2022-08) Chakraborty, Amrita; Chakraborty, Shamik
Matrix 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.
IR spectra of in Ar and cryomatrices: Evidence of unusual band splitting in matrix
(Elsevier, 2022-08) Chakraborty, Amrita; Chakraborty, Shamik
Matrix 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.
Mapping allosteric rewiring in viral RNA: sequence-encoded control of protein binding mechanisms
(2025) Chakraborty, Amrita
RNA 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.
Matrix-isolation FTIR spectroscopic study and quantum chemical calculations of 1:1 adduct of CHCl3 and C2H5OH in N2 matrix
(Elsevier, 2024-06) Chakraborty, Amrita; Chakraborty, Shamik
[Image 1-Image 2] mixture is a common binary solvent used in industries, organic synthesis, lipid extraction, drug extraction, etc. The purpose of this study is to have a molecular level understanding of the interaction of Image 1 with Image 2. The experiments have been carried out in low temperature Image 3 matrix using Fourier Transform Infrared spectroscopy. Electronic structure calculations have been performed to identify the possible binding motifs between Image 1 and Image 2. Three minima have been obtained on the dimer potential energy surface stabilised by Image 4 and Image 5 hydrogen bond, and Image 6 halogen bond interactions. Formation of more than one complexes have been confirmed using the experimental and simulated IR spectra. Energy decomposition analysis and Natural bond orbital analysis have been performed to understand the nature of interaction and the driving force for complexation. This is one of the first reports where separate complexes have been identified between Image 1 and anti and gauche conformers of Image 2 in the low temperature matrix.
Matrix-isolation IR spectroscopy and quantum chemical characterisation of SOCl2 and [SOCl2 single bondHCl] clusters
(Elsevier, 2025-11) Chakraborty, Amrita; Chakraborty, Shamik
The 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.
Organic components modulate the morphology of respirable aerovirology-relevant aerosols
(2026-01) Chakraborty, Amrita
Airborne 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.