Browsing by Author "Chakraborty, Shamik"

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Aggregation induced phosphorescence’ active iridium(iii) complexes for integrated sensing and inhibition of bacterial growth in aqueous solution
(RSC, 2015) Panwar, Jitendra; Laskar, Inamur Rajaman; Chakraborty, Shamik
The present study attempts to develop a sensitive method to utilize ‘aggregation induced phosphorescence (AIP)’ active iridium(III) complexes as potential agents for “integrated” sensing and inhibition of bacterial growth in aqueous systems. The utilization of iridium(III) complexes for microbial detection in bodies of water has been demonstrated using Escherichia coli (E. coli) as a representative bacterial strain. The tested iridium(III) complexes also exhibited antibacterial properties against representative Gram positive and Gram negative bacterial strains with minimum inhibitory concentration (MIC) values of 4 and 8 μg mL−1, respectively. Microscopic observations indicated that these complexes could penetrate into the bacterial cells and result in subsequent cell death. Preliminary mechanistic studies showed that the DNA binding ability of the iridium(III) complexes is responsible for their antibacterial properties. The observed “dual” role in detection as well as inhibition of bacterial growth makes this study highly promising and encouraging for the exploration of the applicability of other less expensive metal complexes for monitoring and controlling the bacterial levels in drinking and sea water systems at a commercial level.
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.
ChandranHaridas. Research Signpost, Trivandrum, IndiaStructure of polyatomic molecules and clusters
(2011) Chakraborty, Shamik
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.
Computational study of red- and blue-shifted Csingle bondH⋯Se hydrogen bond in Q3Csingle bondH⋯SeH2 (Q = Cl, F, H) complexes
(Elsiever, 2018-01) Chakraborty, Shamik
This work presents Csingle bondH⋯Se hydrogen bonding interaction at the MP2 level of theory. The system Q3Csingle bondH⋯SeH2 (Q = Cl, F, and H) provides an opportunity to investigate red- and blue-shifted hydrogen bonds. The origin of the red- and blue-shift in Csingle bondH stretching frequency has been investigated using Natural Bond Orbital analysis. A large amount of electron density is being transferred to the σ∗Csingle bondH orbital in red-shifted Cl3Csingle bondH⋯SeH2. Electron density transfer in the blue-shifted F3Csingle bondH⋯SeH2 is primarily to the remote fluorine atoms. Further, due to polarization of the Csingle bondH bond, the contradicting effects of rehybridization and hyperconjugation are important. The extent of hyperconjugation reigns predominant in explaining the nature of the Csingle bondH⋯Se hydrogen bond in Q3Csingle bondH⋯SeH2 complexes as the hydrogen bond acceptor remain same in this investigation. Red- and blue-shift in Q3Csingle bondH⋯SeH2 (Q = Cl and F) complexes is best described by pro-improper hydrogen bond donor concept.
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 and vibrational spectra of protonated benzaldehyde-water clusters, [BZ-(H2O)n≤5]H+: Evidence for ground-state proton transfer to solvent for n ≥ 3
(AIP, 2014-02-17) Chakraborty, Shamik
Vibrational and electronic photodissociation spectra of mass-selected protonated benzaldehyde-(water)n clusters, [BZ-(H2O)n]H+ with n ≤ 5, are analyzed by quantum chemical calculations to determine the protonation site in the ground electronic state (S0) and ππ* excited state (S1) as a function of microhydration. IR spectra of [BZ-(H2O)n]H+ with n ≤ 2 are consistent with BZH+-(H2O)n type structures, in which the excess proton is localized on benzaldehyde. IR spectra of clusters with n ≥ 3 are assigned to structures, in which the excess proton is located on the (H2O)n solvent moiety, BZ-(H2O)nH+. Quantum chemical calculations at the B3LYP, MP2, and ri-CC2 levels support the conclusion of proton transfer from BZH+ to the solvent moiety in the S0 state for hydration sizes larger than the critical value nc = 3. The vibronic spectrum of the S1 ← S0 transition (ππ*) of the n = 1 cluster is consistent with a cis-BZH+-H2O structure in both electronic states. The large blueshift of the S1 origin by 2106 cm−1 upon hydration with a single H2O ligand indicates that the proton affinity of BZ is substantially increased upon S1 excitation, thus strongly destabilizing the hydrogen bond to the solvent. The adiabatic S1 excitation energy and vibronic structure calculated at the ri-CC2/aug-cc-pVDZ level agrees well with the measured spectrum, supporting the notion of a cis-BZH+-H2O geometry. The doubly hydrated species, cis-BZH+-(H2O)2, does not absorb in the spectral range of 23 000–27 400 cm−1, because of the additional large blueshift of the ππ* transition upon attachment of the second H2O molecule. Calculations predict roughly linear and large incremental blueshifts for the ππ* transition in [BZ-(H2O)n]H+ as a function of n. In the size range n ≥ 3, the calculations predict a proton transfer from the (H2O)nH+ solvent back to the BZ solute upon electronic ππ* excitation.
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.
Experimental evidence of O–H—S hydrogen bonding in supersonic jet
(AIP, 2008-10-13) Chakraborty, Shamik
Experimental evidence is presented for the O–H—S hydrogen bonding in the complexes of simple model compounds of methionine (dimethyl sulphide) and tyrosine (phenol, 𝑝-cresol, and 2-naphthol). The complexes were formed in the supersonic jet and were detected using resonantly enhanced multiphoton ionization spectroscopy. In all the complexes, the band origins for the 𝑆1-𝑆0 electronic transition were redshifted relative to that of their respective monomers. The resonant ion depletion IR spectra of all the complexes show redshifts of 123–140 cm−1 in the O–H stretching frequency, indicating that the OH group acts as the hydrogen bond donor and sulfur as an acceptor. The density functional theory calculations also predict the stable structures in support of this and predict the redshifted O–H stretching frequency in the complex. The atoms-in-molecules and natural bond orbital calculations confirm the O–H—S hydrogen bonding interaction. The significant finding of this study is that the magnitudes of redshifts in the O–H stretch in the O–H—S hydrogen bonded complexes reported here are comparable to those reported for the O–H—O hydrogen bonded complexes where H2O acts as the H-bond acceptor, which suggests that the OH–S interaction is perhaps as strong as the OH–O interaction. To the best of our knowledge, this is the first such report on the O–H—S hydrogen bonded complexes.
An Experimental Exploration of C−H⋅⋅⋅X Hydrogen Bond in [CHCl3−X(CH3)2] Complexes (X=O, S, and Se)
(Wiley, 2023-05) Chakraborty, Shamik
Among the conglomeration of hydrogen bond donors, the C−H group is prevalent in chemistry and biology. In the present work, CHCl3 has been selected as the hydrogen bond donor and are X(CH3)2 are the hydrogen bond acceptors. Formation of C−H⋅⋅⋅X hydrogen bond under the matrix isolation condition is confirmed by the observation of red-shift in the C−H stretching frequency of CHCl3 and comparison with the simulated spectra. Stabilisation energy of all the three complexes is almost equal although the observed red-shift for the C−H⋅⋅⋅O complex is less compared to the C−H⋅⋅⋅S/Se complexes. The nature and origin of the hydrogen bond have been delineated using Natural Bond Orbital, Atoms in Molecules, Non-Covalent Interaction analyses, and Energy Decomposition Analysis. Charge transfer is found to be proportional to the observed red-shift. This work provides the first impression of C−H⋅⋅⋅Se hydrogen bond and its comparison with C−H⋅⋅⋅O/S hydrogen bond interaction under experimental condition.
An Exploration of the Hydrogen Bond Donor Ability of Ammonia
(Wiley, 2023-07) Chakraborty, Shamik
Ammonia is an important molecule due to its wide use in the fertiliser industry. It is also used in aminolysis reactions. Theoretical studies of the reaction mechanism predict that in reactive complexes and transition states, ammonia acts as a hydrogen bond donor forming N−H⋅⋅⋅O hydrogen bond. Experimental reports of N−H⋅⋅⋅O hydrogen bond, where ammonia acts as a hydrogen bond donor are scarce. Herein, the hydrogen bond donor ability of ammonia is investigated with three chalcogen atoms i. e. O, S, and Se using matrix isolation infrared spectroscopy and electronic structure calculations. In addition, the chalcogen bond acceptor ability of ammonia has also been investigated. The hydrogen bond acceptor molecules used here are O(CH3)2, S(CH3)2, and Se(CH3)2. The formation of the 1 : 1 complex has been monitored in the N−H symmetric and anti-symmetric stretching modes of ammonia. The nature of the complex has been delineated using Atoms in Molecules analysis, Natural Bond Orbital analysis, and Energy Decomposition Analysis. This work presents the first comparison of the hydrogen bond donor ability of ammonia with O, S, and Se.
Gas phase IR spectra of tri-peptide Z-Pro-Leu-Gly: Effect of C-terminal amide capping on secondary structure
(Elsiever, 2012-04-02) Chakraborty, Shamik
Three-residue peptides capped with benzyloxycarbonyl (Z-) group, Z-Pro-Leu-Gly–NH2 and Z-Pro-Leu-Gly–OH, are investigated by infrared (IR) spectroscopy, using supersonic-jet laser desorption technique, in the N–H and O–H stretching frequency ranges. The IR spectra show clear evidence of the formation of different hydrogen-bonding network in the two peptides. The possible gas phase structure is proposed from density functional theory calculations using cc-pVDZ basis set. The Z-Pro-Leu-Gly–OH in the gas phase forms successive γ-turn structure with free C-terminal carboxyl group whereas main structural element in Z-Pro-Leu-Gly–NH2 is β-turn with C-terminal single bondNH2 group forming hydrogen bond. Structural information is employed to predict their binding capability in gas phase
Gas Phase Spectroscopic Studies of Hydroquinone Dimer
(ACS, 2004-09-23) Chakraborty, Shamik
Hydroquinone is one of the molecules that forms organic inclusion compounds, which have a wide range of commercial and technological applications. A lot of work has been done on this important molecule in the solid phase, but so far no work has been reported on its homoclusters in the gas phase. We report here the spectroscopic study of the hydroquinone dimer carried out under the jet-cooled conditions using the resonantly enhanced multiphoton ionization (REMPI) technique. The REMPI spectrum was quite rich in terms of the low-frequency transitions indicative of substantial geometry change upon excitation. The number of possible conformers formed in the jet was identified using the hole-burning spectroscopy. Ab initio calculations at the Hartree−Fock, density functional theory level using B3LYP functional and MP2 level for the ground state and the CIS level for the first excited state were carried out to understand the Franck−Condon activity in the spectrum as well as the number of possible stable conformers.
Gas-phase spectroscopy and anharmonic vibrational analysis of the 3-residue peptide Z-Pro-Leu-Gly-NH2 by the laser desorption supersonic jet technique
(Elsiever, 2013-06-20) Chakraborty, Shamik
The electronic excitation and infrared (IR) spectra of a capped tri-peptide, Z-PLG-NH2 (Z = benzyloxycarbonyl, P = Pro, L = Leu, G = Gly), were measured in the gas phase by using the laser desorption supersonic jet technique. By measuring an ultraviolet–ultraviolet hole burning spectrum, it was found that Z-PLG-NH2 has the maximum three conformers in the gas phase, but that the population is mainly distributed to a single conformation. Molecular dynamics simulations and density functional theory calculations well-reproduced the observed IR spectrum, except for splitting of the NH stretching bands by a β-turn structure that corresponds to a global minimum structure. Anharmonic vibrational analysis by vibrational quasi-degenerate perturbation theory (VQDPT) successfully reproduced the anharmonic splitting, and confirmed the assignments.
Gas-Phase Spectroscopy of Synephrine by Laser Desorption Supersonic Jet Technique
(ACS, 2011-08-06) Chakraborty, Shamik
In our previous work, we found that synephrine has six conformers in the gas phase, while adrenaline, which is a catecholamine and has the same side chain as synephrine, has been reported to have only two conformers. To determine the conformational geometries of synephrine, we measured resonance enhanced multiphoton ionization, ultraviolet–ultraviolet hole burning, and infrared dip spectra by utilizing the laser desorption supersonic jet technique. By comparing the observed infrared spectra with theoretical ones, we assigned geometries except for the orientations of the phenolic OH group. Comparison between the determined structures of synephrine and those of 2-methylaminno-1-phenylethanol, which has the same side chain as synephrine but no phenol OH group, leads to the conclusion that the phenolic OH group in synephrine does not affect the conformational flexibility of the side chain. In the case of adrenaline, which is expected to have 12 conformers if there are no interactions between the catecholic OH groups and the side chain, some interactions possibly exist between them because only two conformations are observed. By estimation of the dipole–dipole interaction energy between partial dipole moments of the catecholic OH groups and the side chain, it was concluded that the dipole–dipole interaction stabilizes specific conformers which are actually observed.
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.
Identification of two conformers of 5-indanol in a supersonic free jet
(Elsiever, 2007-07-06) Chakraborty, Shamik
Two conformational isomers of 5-indanol have been identified in a supersonic jet expansion and their S0 ↔ S1 vibronic spectra have been investigated using laser induced fluorescence excitation, dispersed fluorescence and UV–UV hole-burning spectroscopy. Two conformational isomers appear due to the orientation of the –OH group at the 5-position of the benzene ring. The puckering C(1)H2 frequency has been assigned with the aid of theoretical calculations. The experimental observations have been interpreted by the predicts of ab initio electronic structure calculations performed at the HF/6-31+G and MP2/6-31G level of theories.
Infrared and electronic spectra of microhydrated para-dichlorobenzene cluster cations
(Elsiever, 2010-01) Chakraborty, Shamik
Microhydrated para-dichlorobenzene cation clusters, pDCB+single bond(H2O)n with n = 1 and 2, were characterised in the electronic ground state by infrared photodissociation spectroscopy in the O–H and C–H stretch ranges and B3LYP/6–311++G∗∗ calculations. The intermolecular pDCB+single bondH2O potential features at least two nonequivalent minima with charge-dipole configuration and comparable binding energies. The pDCB+single bond(H2O)2 spectrum reveals the presence of two types of isomers, in which either a (H2O)2 dimer or two single H2O ligands are attached to pDCB+. The detected pDCB+single bond(H2O)1,2 complexes are unreactive with respect to nucleophilic substitution. This conclusion is supported for pDCB+single bondH2O by the electronic spectrum of its B ← X transition.