C–H···π Interactions and the Nature of the Donor Carbon Atom

Mishra, Brijesh Kumar; Deshmukh, Milind M.; Ramanathan, V.

doi:10.1021/jo501251s

Cited by 18 publications

(7 citation statements)

References 51 publications

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“…It is worth noting that carbon-centered cationic intermediates are common in both terpene biosynthetic pathways, where C–H/π interactions are known to be catalytic, and in enzymatic depurination of DNA. This observation lends credence to the assertion that C–H/π interactions may be catalytic in DNA repair beyond just the AlkD system, as there exists a preponderance of C–H/π interactions among DNA-binding proteins. , Along these lines, the strongest C–H/π interactions occur when π-rich aryl systems function as Lewis bases, donating electron density to positively polarized hydrogen atoms. − As evinced by proton NMR chemical shift values, endo- and exocyclic oxygen atoms serve to polarize C–H bonds around the deoxyribose ring, making deoxyribose a suitable C–H donor even in an intact nucleotide (i.e., before depurination). Furthermore, the indole moiety of tryptophan residues is an extremely π-rich aryl system, rendering the pairing between tryptophan residues and nucleic acids particularly well-suited to engage in chemically useful C–H/π interactions. , …”

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confidence: 70%

“…7,8 Along these lines, the strongest C-H/π interactions occur when π-rich aryl systems function as Lewis bases, donating electron density to positively polarized hydrogen atoms. 21,22,23 As evinced by proton NMR chemical shift values, 24 endo- and exocyclic oxygen atoms serve to polarize C-H bonds around the deoxyribose ring, making deoxyribose a suitable C-H donor even in an intact nucleotide (i.e., before depurination). Furthermore, the indole moiety of tryptophan residues is an extremely π-rich aryl system, rendering the pairing between tryptophan residues and nucleic acids particularly well-suited to engage in chemically useful C-H/π interactions.…”

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confidence: 99%

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A Catalytic Role for C–H/π Interactions in Base Excision Repair by Bacillus cereus DNA Glycosylase AlkD

et al. 2016

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DNA glycosylases protect genomic integrity by locating and excising aberrant nucleobases. Substrate recognition and excision usually takes place in an extrahelical conformation, which is often stabilized by π-stacking interactions between the lesion nucleobase and aromatic side chains in the glycosylase active site. Bacillus cereus AlkD is the only DNA glycosylase known to catalyze base excision without extruding the damaged nucleotide from the DNA helix. Instead of contacting the nucleobase itself, the AlkD active site interacts with the lesion deoxyribose through a series of C-H/π interactions. These interactions are ubiquitous in protein structures, but evidence for their catalytic significance in enzymology is lacking. Here, we show that the CH/π interactions between AlkD and the lesion deoxyribose participate in catalysis of glycosidic bond cleavage. This is the first demonstration of a catalytic role for C-H/π interactions as intermolecular forces important to DNA repair.

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confidence: 70%

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confidence: 99%

A Catalytic Role for C–H/π Interactions in Base Excision Repair by Bacillus cereus DNA Glycosylase AlkD

et al. 2016

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“…Being general in nature, the MTA-based method can be employed for exploring other intramolecular interactions such as π···π [ 119 ], C-H···π [ 120 ], the so-called halogen bonds [ 121 ], dihydrogen bonds [ 122 ], sulfur bonds [ 123 ], metal-H···S and metal-H···Se bonds [ 124 ], etc. Although identified in the recent literature by these labels, they are cut from the same cloth called the non-covalent interactions .…”

Section: Summary and Concluding Remarksmentioning

confidence: 99%

Molecular Tailoring Approach for the Estimation of Intramolecular Hydrogen Bond Energy

Deshmukh

Gadre

2021

Molecules

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Hydrogen bonds (HBs) play a crucial role in many physicochemical and biological processes. Theoretical methods can reliably estimate the intermolecular HB energies. However, the methods for the quantification of intramolecular HB (IHB) energy available in the literature are mostly empirical or indirect and limited only to evaluating the energy of a single HB. During the past decade, the authors have developed a direct procedure for the IHB energy estimation based on the molecular tailoring approach (MTA), a fragmentation method. This MTA-based method can yield a reliable estimate of individual IHB energy in a system containing multiple H-bonds. After explaining and illustrating the methodology of MTA, we present its use for the IHB energy estimation in molecules and clusters. We also discuss the use of this method by other researchers as a standard, state-of-the-art method for estimating IHB energy as well as those of other noncovalent interactions.

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“…A very accurate interaction energy and potential energy surface for T-shaped (ΔE = −7.2 kcal/mol) and stacked (ΔE = −9.2 kcal/mol) benzene trimers at MP2.5/aug-cc-pVTZ level was presented, and the method was extensively applied to other small noncovalent vdW clusters/complexes. Mishra and co-workers 35 studied the effect of various types of donors on the strength of the C−H•••π interaction, wherein the benzene moiety is the C−H acceptor. There are many studies on the evaluation of stabilization energies of clusters of benzene and other aromatic molecules.…”

Section: Introductionmentioning

confidence: 99%

Molecular Tailoring Approach for Estimating Individual Intermolecular Interaction Energies in Benzene Clusters

et al. 2021

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There is no general method available for the estimation of individual intermolecular interaction energies in weakly bound molecular clusters, and such studies are limited only to the dimer. Recently, we proposed a molecular tailoring approach-based method for the estimation of individual O–H···O hydrogen bond energies in water clusters. In the present work, we extend the applicability of this method for estimating the individual intermolecular interaction energies in benzene clusters, which are expected to be small. The basis set superposition error (BSSE)-corrected individual intermolecular interaction energies in linear (LN) benzene clusters, LN-(Bz) n n = 3–7, were calculated to be in the range from −1.75 to −2.33 kcal/mol with the cooperativity contribution falling between 0.05 and 0.20 kcal/mol, calculated at the MP2.5/aug-cc-pVDZ level of theory. In the case of non-linear (NLN) benzene clusters, NLN-(Bz) n n = 3–5, the BSSE-corrected individual intermolecular interaction energies exhibit a wider range from −1.16 to −2.55 kcal/mol with cooperativity contribution in the range from 0.02 to −0.61 kcal/mol. The accuracy of these estimated values was validated by adding the sum of interaction energies to the sum of monomer energies. These estimated molecular energies of clusters were compared with their actual calculated values. The small difference (<0.3 kcal/mol) in these two values suggests that our estimated individual intermolecular interaction energies in benzene clusters are quite reliable.

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C–H···π Interactions and the Nature of the Donor Carbon Atom

Cited by 18 publications

References 51 publications

A Catalytic Role for C–H/π Interactions in Base Excision Repair by Bacillus cereus DNA Glycosylase AlkD

A Catalytic Role for C–H/π Interactions in Base Excision Repair by Bacillus cereus DNA Glycosylase AlkD

Molecular Tailoring Approach for the Estimation of Intramolecular Hydrogen Bond Energy

Molecular Tailoring Approach for Estimating Individual Intermolecular Interaction Energies in Benzene Clusters

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