Browsing by Author "I. Karmakar"

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Conformational and vibrational spectroscopic investigation of N-n‑butyl, S-2-nitro-1-(p-tolyl)ethyl dithiocarbamate – a bio-relevant sulfur molecule
(Elsevier B.V., 2021) T. Yadav; G. Brahmachari; I. Karmakar; P. Yadav; A.K. Prasad; A. Pathak; A. Agarwal; R. Kumar; V. Mukherjee; G.N. Pandey; R.R.F. Bento; N.P. Yadav
This work describes the synthesis, conformational, thermodynamics and vibrational spectroscopic studies of N-n‑butyl, S-2-nitro-1-(p-tolyl)ethyl dithiocarbamate, a bio-relevant sulfur molecule. A total of seven low lying energy structures of N-n‑butyl, S-2-nitro-1-(p-tolyl)ethyl dithiocarbamate are theoretically predicted. The quantum chemical calculations were performed using Gaussian09 with the 6–31++G(d,p) basis set. This basis set has been shown to reproduce the experimental structural and vibrational properties of N-n‑butyl, S-2-nitro-1-(p-tolyl)ethyl dithiocarbamate. The infrared spectrum was recorded from sample in Kbr pellet in the range 400 to 4000cm−1 with a spectral resolution of 4cm−1and this correlates well with the theoretical spectra of the most stable conformer. The potential energy distribution of the most stable conformer was calculated by employing the normal coordinate analysis method. The natural bond orbital analysis (NBO) of the most stable conformer was done to study the donor-acceptor interactions and stability of the electronic structure. The different thermodynamical parameters, viz, entropy, specific heat, free and thermal energy are also estimated and discussed. The frontier bond orbital analysis has been studied to explore the transition profile of the molecule. Moreover, the structure-property relationship and molecular docking study with methyltransferase group of enzymes have been performed. © 2021 Elsevier B.V.
Conformational Search and Spectroscopic Analysis of Biorelevant Molecule: 5-Chloro-2-hydroxy-N-isobutyl-3-oxo-2,3-dihydrobenzofuran-2-carboxamide
(Taylor and Francis Ltd., 2023) A.K. Vishwkarma; T. Yadav; G. Brahmachari; I. Karmakar; P. Yadav; S. Saha; C. Mahapatra; G.N. Pandey; C.S.P. Tripathi; P.K. Tripathi; V.K. Verma; A. Pathak
The present communication deals with the conformational, vibrational spectroscopic analysis and molecular docking study of an important biorelevant molecule namely 5-Chloro-2-hydroxy-N-isobutyl-3-oxo-2,3-dihydrobenzofuran-2-carboxamide. We have recorded FTIR spectrum of the target molecule in the spectral range of 4000–400 cm−1 and this has been correlated with simulated spectra of the most stable conformer. Most of the theoretical frequencies showed good agreement with experimental frequencies and a few were modified. The theoretical computations on the target molecule have been performed at well-known DFT/B3LYP level. The 6-31++G(d,p) was incorporated as a conventional basis set during the complete computations. For normal modes analysis, the potential energy distributions of the most stable conformer were calculated by Molvib program. The NBO calculations were performed to ensure stability of electronic structure and to explore intermolecular interactions. Some important thermodynamical parameters have also been investigated. The effect of aqueous media revealed that target molecule becomes slightly more stable in water phase. HOMO-LUMO gap has been computed to be 4.19 eV. © 2022 Taylor & Francis Group, LLC.
Molecular modeling, vibrational dynamics and NBO analysis of a synthetic bio‐relevant warfarin analog
(Elsevier B.V., 2023) T. Yadav; A.K. Vishwkarma; M. Mandal; I. Karmakar; A. Pathak; G. Brahmachari; P.K. Tripathi; A.K. Maddheshiya; N.P. Yadav; C. Mahapatra
We have performed the structural and spectroscopic analysis of a warfarin derivative (3-(1-(4-fluorophenyl)-3-(2-hydroxyphenyl)-3-oxopropyl)-4-hydroxy-2H-chromen-2-one). One-dimensional potential energy scanning (PES) of a warfarin derivative has been performed with the aim of finding low-lying energy conformations of this compound. During PES and other computations, we adopted DFT/B3LYP level along with the prevailing basis set 6-31++G(d,p). The conformational analysis through PES revealed five conformers and the global minima for conformer-4. The structures, IR and Raman spectra of conformers were deducted and the IR spectrum of the most stable conformer was correlated with the experimental FTIR spectrum of the target compound. The potential energy distributions (PEDs) for the most stable conformer was computed by employing the standard normal coordinate analysis (NCA) method in the input of Molvib program. Additionally, the HOMO/LUMO analysis and hyper-conjugative interaction energies of donor-acceptor interactions were calculated using NBO calculations. This conformational and vibrational spectroscopic investigation of the target molecule can be a crucial prerequisite for similar investigations on the target and its closely similar molecules. © 2023 Elsevier B.V.
Structural and vibrational spectroscopic signature of a bio-relevant molecule: (E)-3-(2-(4-methoxyphenyl)hydrazineylidene)chromane-2, 4-dione
(Elsevier B.V., 2023) A. K. Vishwkarma; T. Yadav; E. Shakerzadeh; I. Karmakar; G. Brahmachari; A. Kumar; Pramod K. Singh; M. Srivastava; A. Pathak
The investigation of possible low-lying conformational structures of a bio-relevant molecule named (E)-3-(2-(4-methoxyphenyl)hydrazineylidene)chromane-2, 4-dione in gas phase has been performed with respect to possible dihedral angle. While searching for the possible numbers of conformers of the target molecule, DFT/B3LYP/6-31++G(d,p) level of theory was adopted. We have also recorded FTIR spectra of the target molecule in the range of 4000–400 cm−1, which have been correlated with the theoretically simulated IR spectra of the target molecule. The normal coordinate analysis has been employed to calculate potential energy distributions in order to explore the vibrational dynamics of the target molecule. The natural bond orbital (NBO) computations are also performed. Moreover, HOMO and LUMO analysis has been performed to understand the transition profile. © 2023 Elsevier B.V.
Structural confirmation and spectroscopic signature of N-Allyl-2‑hydroxy-5-methyl-3-oxo-2, 3-dihydrobenzofuran-2-carboxamide and its monohydrate cluster
(Elsevier B.V., 2022) T. Yadav; A.K. Vishwkarma; G. Brahmachari; I. Karmakar; P. Yadav; S. Kumar; C. Mahapatra; J. Chowdhury; R. Kumar; G.N. Pandey; P.K. Tripathi; A. Pathak
We performed optimization of a bio-relevant molecule N-Allyl-2‑hydroxy-5-methyl-3-oxo-2, 3-dihydrobenzofuran-2-carboxamide and its monohydrate cluster in the isolated form. Potential energy scanning for the target molecule was carried out. Consequently, three stable conformers were obtained. The effect of interfusion of a water molecule on energy and vibrational modes of the target molecule was also investigated in the most stable conformer. The electronic structures and vibrational spectra of all the three conformers were computed. The FTIR spectrum of the target molecule was recorded at the spectral width of 4000–400cm−1 which was compared with the theoretically computed spectrum of the most stable conformer. We have computed Raman spectra of all the conformers. All theoretical calculations performed in this investigation were done at DFT/B3LYP level of theory. The standard normal coordinate analysis (NCA) method was used to calculate the potential energy distributions of normal modes of the target molecule and its monohydrate cluster. Moreover, the NBO calculations for the target molecule and its monohydrate cluster were done to determine electronic structures, bond energies, occupancies, HOMO-LUMO and hyper-conjugative interaction energies of donor-acceptor interactions. The enthalpy of formation showed that the formation of the monohydrated cluster is of an exothermic nature. © 2022 Elsevier B.V.
Structural confirmation of biorelevant molecule N-iso-butyl, S-2-nitro-1-phenylethyl dithiocarbamate in gas phase and effect of fluorination
(Elsevier B.V., 2021) T. Yadav; G. Brahmachari; I. Karmakar; P. Yadav; A. Agarwal; V. Mukherjee; B.P. Bag; S. Srivastav; A. Vats; A.K. Prasad; G.N. Pandey; A. Pathak; N.K. Dubey
The present manuscript reports the synthesis, structural confirmation, thermodynamics and vibrational spectroscopic studies of an important biorelevant molecule, named N-iso-butyl, S-2-nitro-1-phenylethyl dithiocarbamate in the gas phase. We have found a total of five low lying energy structures of N-iso-butyl, S-2-nitro-1-phenylethyl dithiocarbamate in the present investigation. All the theoretical computations were done at DFT/B3LYP/6-31++G(d,p) level. The FTIR spectrum of this molecule was recorded in the spectral range of 4000–400 cm−1 and this correlates well with the theoretical spectra of energetically most preferred conformer. The effect of fluorination on the structural parameters and vibrational frequencies of the most stable conformer is also investigated. The normal coordinate analysis was employed to calculate the potential energy distributions of the most stable conformer and the fluorinated structure. Moreover, we have also performed the natural bond orbital analysis (NBO) for the most stable conformer and the fluorinated structure to corroborate the stability of the electronic structure of both the molecules. The different thermodynamical quantities viz entropy, specific heat, free energy and thermal energy are also investigated. © 2020
Synthesis, structural and vibrational spectroscopic investigation of molecules: N-n-butyl, S-2-nitro-1-phenylethyl dithiocarbamate and N-n-butyl, S-2-nitro-1-(4-flurophenyl)ethyl dithiocarbamate
(Elsevier B.V., 2020) T. Yadav; G. Brahmachari; I. Karmakar; P. Yadav; A. Agarwal; V. Mukherjee; A. Pathak; N.K. Dubey
The present work deals with the synthesis as well as molecular modeling and vibrational spectroscopic analysis of two biorelevant molecules, namely N-n-butyl, S-2-nitro-1-phenylethyl dithiocarbamate and N-n-butyl, S-2-nitro-1-(4-flurophenyl)ethyldithiocarbamate in gas phase. The optimization of the molecular structures of these compounds was performed at Density Functional Theory with exchange functional B3LYP and Hartree-Fock theory. The customary basis set 6-31++G(d,p) was employed during computations at both the level. The experimental FTIR spectra of both thecompounds were recorded in range 4000–400 cm-1 to correlate with the calculated spectra of the compounds. The normal coordinate analysis (NCA) method was used for the calculation of potential energy distributions. Most of the DFT calculated frequencies were found to agree with the experimental FTIR frequencies. To ensure the stability of electronic structures of these compounds the natural bond orbital analysis (NBO) for each compound was also performed and the analysis revealed that the intramolecular interactions resulting from overlapping of bonding and antibonding orbitals provoke the intramolecular charge transfer (ICT) causing stabilization of the system. The frontier bond orbital analysis was also performed to study the interaction profile of the compounds. © 2020 Elsevier B.V.