Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking

Jena, Subhrakant; Dutta, Juhi; Tulsiyan, Kiran Devi; Sahu, Akshay Kumar; Choudhury, Shubhranshu Shekhar; Biswal, Himansu S.

doi:10.1039/d2cs00133k

Cited by 111 publications

(85 citation statements)

References 175 publications

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“…23,74 A downfield shift in 1 H NMR is a signature of the formation of H-bonded dimers. 36 The downfield 1 †). We also found a linear correlation between the redshift of the X-H stretching frequencies and the donor-acceptor orbital overlap energies (Fig.…”

Section: Spectroscopic Signature For Hydrogen Bonds With Tellurium An...mentioning

confidence: 99%

“…Noncovalent interactions (NCIs) play a vital role in biomolecules and crystal engineering. [1][2][3] The conventional N-HÁ Á ÁO, O-HÁ Á ÁO, N-HÁ Á ÁN, O-HÁ Á ÁN, and C-HÁ Á ÁC hydrogen bonds (H-bonds) are the most important NCIs in supramolecular chemistry and structural biology. [4][5][6][7][8][9] These H-bonds are strong and mostly driven by the electronegativity differences between the donor and acceptor atoms.…”

Section: Introductionmentioning

confidence: 99%

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Hydrogen bonding with polonium

Tulsiyan

Jena

Dutta

et al. 2022

Phys. Chem. Chem. Phys.

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Section: Spectroscopic Signature For Hydrogen Bonds With Tellurium An...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Hydrogen bonding with polonium

Tulsiyan

Jena

Dutta

et al. 2022

Phys. Chem. Chem. Phys.

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“…The PnB is often involved in catalysis [ 27 , 28 ]: some examples include a chiral scaffold [ 29 ], enantioselective transfer hydrogenation of benzoxazines [ 30 ], and polyether cascade cyclizations [ 31 ]. Applications have been studied in terms of halide binding [ 32 , 33 , 34 , 35 ] and as a common factor in biological contexts [ 36 , 37 ] such as proteins and nucleic acids [ 38 ].…”

Section: Introductionmentioning

confidence: 99%

Involvement of Arsenic Atom of AsF3 in Five Pnicogen Bonds: Differences between X-ray Structure and Theoretical Models

2022

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Bonding within the AsF3 crystal is analyzed via quantum chemical methods so as to identify and quantify the pnicogen bonds that are present. The structure of a finite crystal segment containing nine molecules is compared with that of a fully optimized cluster of the same size. The geometries are qualitatively different, with a much larger binding energy within the optimized nonamer. Although the total interaction energy of a central unit with the remaining peripheral molecules is comparable for the two structures, the binding of the peripherals with one another is far larger in the optimized cluster. This distinction of much stronger total binding within the optimized cluster is not limited to the nonamer but repeats itself for smaller aggregates as well. The average binding energy of the cluster rises quickly with size, asymptotically approaching a value nearly triple that of the dimer.

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“…70 In addition, computational studies can also provide information on how different types of noncovalent interactions modulate the catalytic reaction pathways. 68,69,75,76 Since this reaction happens in water, and the catalyst possesses hydrogen bonding sites, it is expected that hydrogen bonding has an important role in this catalytic reaction. Herein, we have designed a synthesis strategy for the ChOHassisted coupling of nucleophilic acetone with an electrophilic aromatic aldehyde to produce α,β-unsaturated ketones.…”

Section: ■ Introductionmentioning

confidence: 99%

Synthesis of α,β-Unsaturated Ketones in Water: The Claisen–Schmidt Condensation Revisited

Choudhury

Mahapatra

Sahu

et al. 2022

ACS Sustainable Chem. Eng.

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Carrying out organic synthesis in an aqueous medium is always challenging. Herein, we present a highly efficient method for the synthesis of α,β-unsaturated ketones in water through the Claisen−Schmidt condensation by using a green catalyst, choline hydroxide (ChOH). The products were isolated without any chromatographic separation technique. The catalyst shows high substrate tolerance and works well with electrondonating and electron-withdrawing substituted aromatic aldehydes. Not only is the catalyst metal-free and nontoxic, but it also offers the advantage of forming strong hydrogen bonds with the transition state and intermediates, facilitating the reaction and enhancing the product yield. A variety of substrate scopes has been explored. The catalysis happens at 50 °C in water which is the significant finding of this study. The reaction mechanism of this hydrogen-bond-mediated catalysis was thoroughly investigated with density functional theory (DFT). The plausible reaction pathway was proposed based on the energetics of the reactants, intermediates, transition states, and product. Further, quantum theory of atoms in molecules (QTAIM) and noncovalent interactions (NCI) index analyses were done to demonstrate the effects of strong hydrogen bonds in the crucial steps of the reaction pathway. The obtained results correlate well with our hypothesis and validate our proposed mechanism, suggesting that the hydrogen-bond-mediated catalysis needs special attention in carrying out organic synthesis in water.

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Noncovalent interactions in proteins and nucleic acids: beyond hydrogen bonding and π-stacking

Abstract: This review presents a summary of seven noncovalent interactions (NCIs) that are prevalent in proteins and nucleic acids. These NCIs are belittled in the literature and need special attention.

Cited by 111 publications

References 175 publications

Hydrogen bonding with polonium

Hydrogen bonding with polonium

Involvement of Arsenic Atom of AsF3 in Five Pnicogen Bonds: Differences between X-ray Structure and Theoretical Models

Synthesis of α,β-Unsaturated Ketones in Water: The Claisen–Schmidt Condensation Revisited

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