The role of hyperconjugation in the unusual conformation of thymine: A natural bond orbital analysis

Rengifo, Emerson; Gómez, Sara; Arce, J. C.; Weinhold, Frank; Restrepo, Albeiro

doi:10.1016/j.comptc.2018.03.005

Cited by 7 publications

(6 citation statements)

References 30 publications

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“…Following the procedures introduced in a previous study of virus•••cell intermolecular interactions for the wild-type SARS-COV-2, [15] the strength of bonding interactions is described and quantified in terms of a set of QTAIM (first three items below) and NBO indexes rooted in quantum chemistry and firmly linked to the physicochemical nature of the interaction. In particular, [19][20][21][22][23][24][25][26] (i) Accumulation of electron densities at the bond critical points for intermolecular contacts. Larger densities indicate stronger interactions.…”

Section: Introductionmentioning

confidence: 99%

The Role of Spike Protein Mutations in the Infectious Power of SARS‐COV‐2 Variants: A Molecular Interaction Perspective

et al. 2021

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Specific S477N, N501Y, K417N, K417T, E484K mutations in the receptor binding domain (RBD) of the spike protein in the wild type SARS‐COV‐2 virus have resulted, among others, in the following variants: B.1.160 (20A or EU2, first reported in continental Europe), B1.1.7 (α or 20I501Y.V1, first reported in the United Kingdom), B.1.351 (β or 20H/501Y.V2, first reported in South Africa), B.1.1.28.1 (γ or P.1 or 20J/501Y.V3, first reported in Brazil), and B.1.1.28.2 (ζ, or P.2 or 20B/S484K, also first reported in Brazil). From the analysis of a set of bonding descriptors firmly rooted in the formalism of quantum mechanics, including Natural Bond Orbitals (NBO), Quantum Theory of Atoms In Molecules (QTAIM) and highly correlated energies within the Domain Based Local Pair Natural Orbital Coupled Cluster Method (DLPNO‐CCSD(T)), and from a set of computed electronic spectral patterns with environmental effects, we show that the new variants improve their ability to recognize available sites to either hydrogen bond or to form salt bridges with residues in the ACE2 receptor of the host cells. This results in significantly improved initial virus⋅⋅⋅cell molecular recognition and attachment at the microscopic level, which trigger the infectious cycle.

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Section: Introductionmentioning

confidence: 99%

The Role of Spike Protein Mutations in the Infectious Power of SARS‐COV‐2 Variants: A Molecular Interaction Perspective

et al. 2021

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“…Weinhold and co‐workers have utilized the NBO‐theory to analyze the structural diversity for a wide range of molecules. Recently, Nori‐Shargh and Weinhold have tried to bridge between PJT theory and NBO theory . In this article, we have further explored the suitability of NBO based analyses for identifying and qualitatively assessing the importance of PJT effects in the molecular analog of silicene, hexasilabenzene (Si 6 H 6 ).…”

Section: Introductionmentioning

confidence: 99%

Analysis of pseudo jahn–teller distortion based on natural bond orbital theory: Case study for silicene

2019

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Ground state (GS) instability of nondegenerate molecules in high symmetric structures is understood through Pseudo Jahn–Teller mixing of the electronic states through the vibronic coupling. The general approach involves setting up of a Pseudo Jahn–Teller (PJT) problem wherein one or more symmetry allowed excited states couple to the GS to create vibrational instability along a normal mode. This faces two major complications namely (1) estimating the adiabatic potential energy surfaces for the excited states which are often difficult to describe in case the excited states have charge‐transfer or multi‐excitonic (ME) character and (2) finding out how many such excited states (all satisfying the symmetry requirements for vibronic coupling) of increasing energies need to be coupled with the GS for a particular PJT problem. An analogous alternative approach presented here for the well‐known case of symmetry breaking of planar (D6h) hexasilabenzene (Si6H6) to the buckled (D3d) structure involves identifying the second‐order donor–acceptor, hyperconjugative interactions (E2i → j) that stabilize the distorted structure. Following the recent work of Nori‐Shargh and Weinhold, one observes that the orbitals involved in the vibronic coupling between the S0/Sn states and those for the donor (filled)–acceptor (empty) interactions are identical. In fact, deletion of any particular pair of E2i → j interaction creates vibrational instability in the buckled structure and as a corollary, deleting it for the planar structure removes its instability. The one‐to‐one correlation between the natural bond orbital theory and PJT theory assists in an intuitive identification of the relevant (few) excited states from a manifold of computed ones that cause symmetry breaking by vibronic coupling. © 2019 Wiley Periodicals, Inc.

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“…This is highly unusual because if eclipsing of bonds occurs, C=O in pyrimidine to C–H in the imidazole methyl eclipsation (structures V–VIII ) should be highly favorable due to a strong inductive effect, although the pyrimidinic carbonyl is four atoms apart so this is not exactly the 1,3-allylic effect [ 13 , 14 ]. This puzzling C–H/C–H in plane eclipsation has already been observed in thymine and was rationalized as being due to hyperconjugation in the form of charge transfer from the aromatic ring to the methyl group and vice versa [ 16 ]. There is also C–H/C=O eclipsing (1,3–allylic effect) in the pyrimidyne ring, however, only one of the methyl groups behaves this way (structures III, IV, VII, VIII ), the second methyl prefers to eclipse a C–N bond in the imidazole ring (structures I, II, V, VI ).…”

Section: Resultsmentioning

confidence: 97%

“…Notice that all methyl groups have different chemical environments and thus each internal rotation must be analyzed in detail. Within caffeine, methyl rotations are heavily influenced among other factors by the 1,3–allylic effect [ 13 , 14 ] (M3 is separated by four atoms from the nearest carbonyl group and thus is only affected by remote allylic interactions), by the

density of the heavily conjugated system, by the ability to form intramolecular CH

interactions [ 15 ], and by the well known ability of C–H bonds in methyl groups to eclipse C–H bonds in aromatic planes [ 16 , 17 ].…”

Section: Introductionmentioning

confidence: 99%

Analysis of Conformational Preferences in Caffeine

2022

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High level DLPNO–CCSD(T) electronic structure calculations with extended basis sets over B3LYP–D3 optimized geometries indicate that the three methyl groups in caffeine overcome steric hindrance to adopt uncommon conformations, each one placing a C–H bond on the same plane of the aromatic system, leading to the C–H bonds eclipsing one carbonyl group, one heavily delocalized C–N bond constituent of the fused double ring aromatic system, and one C–H bond from the imidazole ring. Deletion of indiscriminate and selective non-Lewis orbitals unequivocally show that hyperconjugation in the form of a bidirectional –CH3 ⇆ aromatic system charge transfer is responsible for these puzzling conformations. The structural preferences in caffeine are exclusively determined by orbital interactions, ruling out electrostatics, induction, bond critical points, and density redistribution because the steric effect, the allylic effect, the Quantum Theory of Atoms in Molecules (QTAIM), and the non-covalent interactions (NCI), all predict wrong energetic orderings. Tiny rotational barriers, not exceeding 1.3 kcal/mol suggest that at room conditions, each methyl group either acts as a free rotor or adopts fluxional behavior, thus preventing accurate determination of their conformations. In this context, our results supersede current experimental ambiguity in the assignation of methyl conformation in caffeine and, more generally, in methylated xanthines and their derivatives.

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The role of hyperconjugation in the unusual conformation of thymine: A natural bond orbital analysis

Cited by 7 publications

References 30 publications

The Role of Spike Protein Mutations in the Infectious Power of SARS‐COV‐2 Variants: A Molecular Interaction Perspective

The Role of Spike Protein Mutations in the Infectious Power of SARS‐COV‐2 Variants: A Molecular Interaction Perspective

Analysis of pseudo jahn–teller distortion based on natural bond orbital theory: Case study for silicene

Analysis of Conformational Preferences in Caffeine

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