Structural confirmation and spectroscopic study of a biomolecule: Norepinephrine

Yadav, Tarun; Mukherjee, V.

doi:10.1016/j.saa.2018.05.040

Cited by 13 publications

(12 citation statements)

References 29 publications

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“…[ 32 ] Therefore, it reveals that octopamine possess higher magnitude for this mode that compared to the norepinephrine neurotransmitter. [ 32 ] This mode is coupled mode and reasonable contribution of CC2 stretching, CN stretching, CH in plane bending, CH 2 wagging and twisting modes along with itself. There is a band at 830 cm −1 in neutral octopamine which is attributed to the out of plane bending mode of CH in present study while in the case of its radical the PED reveal this mode contribution at three frequencies below region of 1000 cm ‐1 which are 840, 804 and 727 cm −1 .…”

Section: Resultsmentioning

confidence: 99%

“…The band corresponding to the out of plane bending mode of CH was predicted at 864cm −1 in norepinephrine. [ 32 ] Therefore, this mode shows contribution at higher value that compared to both the octopamine and its radical. The rest mode is also found well within this region and expressed in Tables S2c, S3 (supporting information) respectively for octopamine and octopamine − .…”

Section: Resultsmentioning

confidence: 99%

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Structural Modeling, Spectroscopic Signature and NBO Analysis of Octopamine and Its Radical

Yadav,

Vishwkarma

et al. 2024

Macromolecular Symposia

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The present communication deals with theoretical vibrational spectroscopic signature (IR and Raman) of octopamine molecule and its radical. All theoretical calculations for octopamine and its radical are performed at DFT/B3LYP/6‐31++G (d, p) level. Besides, the vibrational frequencies of these two structures has been compared. Most of the vibrational frequencies agree well with experimental ones. It has been documented how the geometrical characteristics and vibrational frequencies of octopamine are affected when hydrogen is removed from the oxygen atom's site. The HOMO‐LUMO energy gap in the case of neutral form of octopamine is computed to be 5.42 eV while for deprotonated octopamine this gap has been increased by 0.78 eV. The NBO analysis is also performed to ensure stability of radical of octopamine. The magnitude of occupancy at bonding orbitals within the 0.997–0.885e, and 0.996–0.885e range in octopamine and octopamine, respectively, is calculated.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Structural Modeling, Spectroscopic Signature and NBO Analysis of Octopamine and Its Radical

Yadav,

Vishwkarma

et al. 2024

Macromolecular Symposia

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“…The calculated values of NBOs for Baricitinib are shown in Table 1 . The intramolecular interactions within a molecule occurs due to the overlapping between bonding and anti-bonding orbitals which causes intramolecular charge transfer (ICT) resulting in stabilization of the molecule [14] . The charge transfer between bonding orbital σ(C38-H43) and anti-bonding orbital σ*(C23-N24) (7898.57 kJ/mol) is found to be the strongest among all the interactions.…”

Section: Resultsmentioning

confidence: 99%

DFT study on the structural and chemical properties of Janus kinase inhibitor drug Baricitinib

Sonia

Devi

Karlo

2022

Materials Today: Proceedings

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“…(d) The total number of tautomers and conformers we start with is 1139 (260 tautomers +879 conformers). These are obtained based on the conformer ordering from the literature. ,− In references and − , we list the name of the acid followed by the paper wherein we started our conformational sampling. From among these 1139 tautomers and conformers, 705 of them have conformers that are less than 2 kcal/mol (628 conformers and 77 tautomers).…”

Section: Methodsmentioning

confidence: 99%

Accurate Computation of Aqueous pK_as of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method

Pereira,

Ramabhadran

2023

J. Phys. Chem. A

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The use of static electronic structure calculations to compute solution-phase pK as offers a great advantage in that a macroscopic bulk property could be computed via microscopic computations involving very few molecules. There are various sources of errors in the quantum chemical calculations though. Overcoming these errors to accurately compute pK as of a plethora of acids is an active area of research in physical chemistry pursued by both computational as well as experimental chemists. We recently developed the pK-Yay method in our attempt to accurately compute aqueous pK as of strong and weak acids. The method is fully black-box, computationally inexpensive, and is very easy for even a nonexpert to use. However, the method was thus far tested on very few molecules (only 16 in all). Herein, in order to assess the future applicability of pK-Yay, we study the effect of multiple conformers, the presence of tautomers under equilibrium, and the impact of a wide variety of functional groups (derivatives of acetic acid with substituents at various positions, dicarboxylic acids, aromatic carboxylic acids, amines and amides, phenols and thiols, and fluorine bearing organic acids). Starting with more than 1000 conformers and tautomers, this study establishes that overall errors of ∼ 1.0 pK a units are routinely obtained for a majority of the molecules. Larger errors are noted in cases where multiple charges, intramolecular hydrogen bonding, and several ionizable functional groups are simultaneously present. An important conclusion to emerge from this work is that, the computed pK as are insensitive (difference <0.5) to whether we consider multiple conformers/tautomers or only choose the most stable conformer/tautomer. Further, pK-Yay captures the stereoelectronic effects arising due to differing axial vs equatorial pattern, and is useful to predict the dominant acid–base equilibrium in a system featuring several equilibria. Overall, pK-Yay may be employed in several chemical applications featuring organic molecules and biomonomers.

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Structural confirmation and spectroscopic study of a biomolecule: Norepinephrine

Cited by 13 publications

References 29 publications

Structural Modeling, Spectroscopic Signature and NBO Analysis of Octopamine and Its Radical

Structural Modeling, Spectroscopic Signature and NBO Analysis of Octopamine and Its Radical

DFT study on the structural and chemical properties of Janus kinase inhibitor drug Baricitinib

Accurate Computation of Aqueous pK_as of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method

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Structural confirmation and spectroscopic study of a biomolecule: Norepinephrine

Cited by 13 publications

References 29 publications

Structural Modeling, Spectroscopic Signature and NBO Analysis of Octopamine and Its Radical

Structural Modeling, Spectroscopic Signature and NBO Analysis of Octopamine and Its Radical

DFT study on the structural and chemical properties of Janus kinase inhibitor drug Baricitinib

Accurate Computation of Aqueous pKas of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method

Contact Info

Product

Resources

About

Accurate Computation of Aqueous pK_as of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method