Browsing by Author "T. Yadav"

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Computational insights into the adsorption of norepinephrine neurotransmitter onto B12N12 nanocage
(Elsevier Ltd, 2024) T. Yadav; E. Shakerzadeh; S. Goswami; E. Tahmasebi; J. Adam; S. Garai
The present study reports the adsorption behaviour of norepinephrine neurotransmitter onto boron nitride (B12N12) nanocage to explore its suitability for targeted drug delivery. The potential use of B12N12 nanocage for targeted drug delivery of norepinephrine has been analyzed by computing geometrical and electronic properties and adsorption energies in various possible norepinephrine@B12N12 nanohybrids. All quantum chemical calculations for geometry optimization and vibrational frequency analysis have been performed at the DFT/B3LYP/6-311G(d,p) level of theory. Norepinephrine adsorbs onto B12N12 nanocage via C-H···π, N-H···π, O-H···π, O-H···N hydrogen bond, O[sbnd]B and N[sbnd]B dative bonds. The nanohybrid of norepinephrine@B12N12, in its most favourable configuration, offers −33.31 kcal/mol in the gas phase, reflecting the potential of the B12N12 nanocage for drug delivery applications of norepinephrine. The effect of the aqueous medium on adsorption energy and electronic properties of the most favourable nanohybrid has also been investigated. Natural bond orbital (NBO) computations have assessed net charge transfer between norepinephrine and the B12N12 nanocage. Moreover, ab initio molecular dynamics (AIMD) simulations have been performed to ensure the thermal stability of the studied nanohybrid. © 2024 Elsevier B.V.
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.
Enhancement of birefringence for liquid crystal with the doping of ferric oxide nanoparticles
(Elsevier B.V., 2023) P.K. Tripathi; D.P. Singh; T. Yadav; V. Singh; A.K. Srivastava; Y.S. Negi
Electro-optical (E-O) property of nematic liquid crystalline (NLC) materials is the key parameter of display and non-display applications. Optical anisotropy (i.e., birefringence) is one of the critical parameters of these LCs via which E-O properties are governed. In this article, we have investigated the effect of ferric oxide nanoparticles (Fe2O3 NPs) on the birefringence and the order parameter of a NLC when doped into different weight percentages (wt%). The birefringence of the NLC has been examined via the phase modulation optical transmittance technique. It is noticed that the value of birefringence increases with the concentration of NPs in the LC matrix which is analogous to an improved order parameter of NLC after the addition of NPs. The improved ordering of LC molecules has been verified using polarized optical microscopy. This study helps in understanding the guest-host interactions for improved optical applications of LC materials. © 2022 Elsevier B.V.
Gas-phase conformational analysis and vibrational signatures of diphenhydramine: Investigating the interplay with hydrochloride
(Elsevier B.V., 2024) A. Kumari; E. Shakerzadeh; A.K. Maddheshiya; A.K. Vishwkarma; S. Yadav; T. Yadav; S. Chakroborty; K. Pal; J. Malviya; J.A. Sawale; T. Roy; N. Yadav
We have performed a comprehensive analysis of the conformational and vibrational spectroscopic properties of Diphenhydramine in the gas phase using potential energy scanning calculations at DFT/B3LYP/6-31++G(d, p) level of theory which identified three different conformational structures. The influence of hydrochloride (HCl) on the energy profile and vibrational frequencies of the most stable conformational structure was investigated. The presence of HCl showed a decrement in the energy by -460.8312 a.u. confirming DPH–HCl structurally more stable than isolated DPH. Normal coordinate analysis (NCA) was employed to compute the total potential energy distribution for both the most stable conformational structure and the HCl complex. The results indicate that the DFT-computed vibrational frequencies are in good agreement with previously reported values. HOMO and LUMO was conducted to study the transition profile of the molecule. Additionally, NBO calculations were performed to ensure the stability of electronic structures at the same level of theory. © 2023 Elsevier B.V.
Histamine sensing by boron and silicon doped C60 fullerenes: A first principles investigation
(Elsevier Ltd, 2023) T. Yadav; E. Shakerzadeh; A.K. Vishwkarma; Pramod K. Singh; A. Pathak; S. Chakroborty; F.P. Pandey; S. Moharana; R. Kumar
The present study reports adsorption mechanism of histamine on the surfaces of pure, B- or Si-doped fullerenes. The adsorption of histamine on pure and doped fullerenes has been investigated through density functional theory calculations in the terms of stability, geometry, work function, electronic properties, and density of state spectra. The magnitude of adsorption energies has been computed to be −1.66, −35.29, and −37.43 kcal/mol for histamine corresponding to the most favorable adsorption configurations respectively. The band gap analysis revealed that the electrical conductivity of pure fullerene remains nearly constant even after histamine adsorption. However, the doping of boron and silicon leads to the decrease of the band gap after histamine adsorption resulting increment in the electrical conductivity which infers that boron and silicon doped fullerenes are more sensitive towards histamine adsorption than pure fullerene. Moreover, the NBO calculations showed charge transfer of 0.008, 0.409, and 0.272e from histamine to pure, boron and silicon doped fullerenes in the most favorable adsorption configurations, respectively. © 2023 Elsevier B.V.
In silico investigation on interaction of small Ag6 nano-particle cluster with tyramine neurotransmitter
(Nature Research, 2023) Subhendu Chakroborty; E. Shakerzadeh; T. Yadav; Nilima Priyadarsini Mishra; Arundhati Barik; Versha Upadhyay; Abhilasha; Siba Soren; Jitendra Malviya; Amiya Ranjan Panda; Kartik Uniyal; Narendra Kumar; Shradha Wagadre; F.P. Pandey
The interaction of tyramine neurotransmitter with silver nano-particle (Ag6) cluster is explored in terms of the molecular structure, electronic properties and NBO analysis of tyramine-AgNPs bio-molecular conjugate. The adsorption mechanism of tyramine onto the Ag6 cluster has been investigated through computing of the electronic and geometrical properties in addition to the adsorption energies in various possible configurations. The magnitude of adsorption energy corresponding to the most favorable tyramine-Ag6 bio-molecular conjugate has been computed to be − 14.36 kcal/mol in the gas phase, which infers a good adsorption of tyramine with AgNPs cluster suggesting the practical applications of tyramine-AgNPs bio-molecular conjugates in bio-sensing, drug delivery, bio-imaging and other applications. Different electronic properties such as the energy gap of HOMO–LUMO, Fermi level and work function have been investigated in detail. Moreover, the effect of aqueous media on adsorption energy and electronic properties of the most favorable tyramine-AgNPs bio-molecular conjugate is investigated in order to understand the impact of the real biological situation. © 2023, The Author(s).
In silico investigation on molecular modeling of tyramine and its deprotonated form
(Elsevier B.V., 2023) M. Kushal; S. Yadav; T. Yadav; A.K. Vishwkarma; S. Bhushan; R. Kumar; R.V. Yadav; Pankaj K. Tripathi
The present investigation covers structural, thermodynamics and vibrational spectroscopic study of tyramine neurotransmitter and its deprotonated form in the gas phase. The ab initio calculations on both the tyramine and its deprotonated form have been performed at DFT/B3LYP/6-31++G(d,p) level in order to optimize the electronic structures and computation of vibrational frequencies. Besides, the computed frequencies of tyramine and its deprotonated form have been compared with the experimentally reported IR and Raman frequencies which showed that most of the vibrational frequencies are in well agreement with earlier reported data. We have also documented the effect of hydrogen removal from the site of oxygen atom on the theoretically computed vibrational frequencies and geometrical parameters of tyramine. To explore the transition profile frontier bond orbitals energies have been computed. Moreover, natural bond orbital (NBO) calculations have also been performed to ensure stability of optimized electronic structures of tyramine and its deprotonated form. © 2023 Elsevier B.V.
In silico investigation on sensing of tyramine by boron and silicon doped C60 fullerenes
(Nature Research, 2023) S. Pattanaik; A.K. Vishwkarma; T. Yadav; E. Shakerzadeh; D. Sahu; S. Chakroborty; P.K. Tripathi; E.A. Zereffa; J. Malviya; A. Barik; S.K. Sarankar; P. Sharma; V.J. Upadhye; S. Wagadre
The present communication deals with the adsorption of tyramine neurotransmitter over the surface of pristine, Boron (B) and Silicon (Si) doped fullerenes. Density functional theory (DFT) calculations have been used to investigate tyramine adsorption on the surface of fullerenes in terms of stability, shape, work function, electronic characteristics, and density of state spectra. The most favourable adsorption configurations for tyramine have been computed to have adsorption energies of − 1.486, − 30.889, and − 31.166 kcal/mol, respectively whereas for the rest three configurations, it has been computed to be − 0.991, − 6.999, and − 8.796 kcal/mol, respectively. The band gaps for all six configurations are computed to be 2.68, 2.67, 2.06, 2.17, 2.07, and 2.14 eV, respectively. The band gap of pristine, B and Si doped fullerenes shows changes in their band gaps after adsorption of tyramine neurotransmitters. However, the change in band gaps reveals more in B doped fullerene rather than pristine and Si doped fullerenes. The change in band gaps of B and Si doped fullerenes leads a change in the electrical conductivity which helps to detect tyramine. Furthermore, natural bond orbital (NBO) computations demonstrated a net charge transfer of 0.006, 0.394, and 0.257e from tynamine to pristine, B and Si doped fullerenes. © 2023, The Author(s).
Interaction of a synthetic bio-relevant drug-molecule with C24 and B12N12 fullerene: A first-principles quantum chemical investigation
(Elsevier Ltd, 2023) A.K. Vishwkarma; T. Yadav; A. Pathak; G. Brahmachari
This research deals with the interaction of a synthetic bio-relevant drug-molecule with fullerene like nanocages specifically C24 and B12N12 to explore their potential as carrier in drug delivery systems. The efficacy of C24 and B12N12 nanocages as an effective drug carrier has been investigated by computing electronic and geometrical properties along with adsorption energies in different possible configurations. The ab initio calculations have been performed at DFT/B3LYP/6-31G(d, p) level of theory. The adsorption energy for the target molecule over the surface of C24 nanocage in the most favorable configuration has been calculated to be -1.324 kcal/mol. However, the target molecule when adsorbs over the surface of B12N12 nanocage then its adsorption energy is −20.659 kcal/mol for the most favorable configuration in the gas phase, which suggests that B12N12 nanocage can be used as an effective drug carrier for target molecule. In contrast, C24 nanocage due to its low value of adsorption energy cannot be used as a drug carrier for the target molecule. We have computed various electronic properties viz HOMO-LUMO energy gap, Fermi level and work function. Moreover, the effect of aqueous media on these electronic properties and adsorption energy has been explored. © 2022 Elsevier B.V.
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.
Theoretical spectroscopic signature of synephrine using DFT and the effect of hydrogen removal
(Taylor and Francis Ltd., 2022) N.P. Yadav; A.K. Vishwkarma; K. Kumar; A. Vats; A. Pathak; R. Kumar; V. Mukerjee; S. Moharana; T. Yadav; C. Mahapatra; S. Srivastava
The present work deals with the vibrational spectroscopic signature of the synephrine molecule and its radical in the gas phase. We have optimized synephrine and synephrine- in the ground state. The optimization of the neutral and de-protonated synephrine has been performed at the B3LYP/6-31++G(d, p) level of theory. The comparison of vibrational frequencies of both the structures has also been made. Most of the vibrational frequencies are in good agreement with the experimental ones. The effect of hydrogen removal from the site of oxygen atom upon geometrical parameters and vibrational frequencies of synephrine has been reported. Subsequently, the different thermodynamical parameters calculated at room temperature for the synephrine and its radical have been discussed. Interestingly, the enthalpy of formation for the synephrine and deprotonated synephrine has been calculated. The NBO analysis has been performed to check the stability of the electronic structure of the radical form of the synephrine molecule. Also, the HOMO-LUMO energy gap infers that synephrine is more reactive in its radical form. © 2022 Informa UK Limited, trading as Taylor & Francis Group.