Proton transfer in guanine–cytosine base pair analogues studied by NMR spectroscopy and PIMD simulations

Pohl, Radek; Socha, Ondřej; Slavı́ček, Petr; Šála, Michal; Hodgkinson, Paul; Dračínský, Martin

doi:10.1039/c8fd00070k

Cited by 34 publications

(27 citation statements)

References 61 publications

(41 reference statements)

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“…Both tautomers are found in a 1:1 ratio in solid isocytosine, where the basic structural motif contains the hydrogen-bonded dimer of the two isocytosine tautomers [21][22][23]. This isocytosine dimer has also been observed in solution [22,24,25].…”

Section: Methodsmentioning

confidence: 85%

“…Variable-temperature 1 H-NMR spectra were recorded on a Bruker 500 MHz NMR spectrometer ( 1 H at 500.0 MHz) in a 3:1 mixture of dimethylformamide (DMF)-d 7 and CD 2 Cl 2 (referenced to the solvent signal δ = 2.75). The assignment of the signals was based on analogy with previously published data [25].…”

Section: Methodsmentioning

confidence: 99%

“…Isocytosine in solution forms a dimer of hydrogen-bonded 1,2-I and 2,3-I tautomers upon cooling [24,25]. This means that the free-energy gain connected with the dimer formation is larger than the free-energy penalty needed for the formation of the less stable 1,2-I tautomer.…”

Section: Methodsmentioning

confidence: 99%

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Tautomerism of Guanine Analogues

Štoček

Dračínský

2020

Biomolecules

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Tautomerism of nucleic acid (NA) bases is a crucial factor for the maintenance and translation of genetic information in organisms. Only canonical tautomers of NA bases can form hydrogen-bonded complexes with their natural counterparts. On the other hand, rare tautomers of nucleobases have been proposed to be involved in processes catalysed by NA enzymes. Isocytosine, which can be considered as a structural fragment of guanine, is known to have two stable tautomers both in solution and solid states. The tautomer equilibrium of isocytosine contrasts with the remarkable stability of the canonical tautomer of guanine. This paper investigates the factors contributing to the stability of the canonical tautomer of guanine by a combination of NMR experiments and theoretical calculations. The electronic effects of substituents on the stability of the rare tautomers of isocytosine and guanine derivatives are studied by density functional theory (DFT) calculations. Selected derivatives are studied by variable-temperature NMR spectroscopy. Rare tautomers can be stabilised in solution by intermolecular hydrogen-bonding interactions with suitable partners. These intermolecular interactions give rise to characteristic signals in proton NMR spectra, which make it possible to undoubtedly confirm the presence of a rare tautomer.

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Section: Methodsmentioning

confidence: 85%

Section: Methodsmentioning

confidence: 99%

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Tautomerism of Guanine Analogues

Štoček

Dračínský

2020

Biomolecules

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“…22 More generally, quantum tunneling phenomena have been investigated in a variety of chemical contexts, with particular attention to their role in kinetic isotope effects. [30][31][32][33][34][35][36][37][38] Within this framework, the probability of a quantum object such as a proton with an energy smaller than the potential barrier to appear on the other side is taken into account in the evaluation of the apparent rate constant of the process. This probability is greater for particles Cross-term splittings due to the orientational inequivalence of proton magnetic shielding tensors: Do water molecules trapped in crystals hop or tunnel?…”

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confidence: 99%

Cross-term Splittings Due to the Orientational Inequivalence of Proton Magnetic Shielding Tensors: Do Water Molecules Trapped in Crystals Hop or Tunnel?

Carnevale

Pelupessy

Bodenhausen

2019

J. Phys. Chem. Lett.

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Cross-term splittings due to the orientational inequivalence of proton magnetic shielding tensors: Do water molecules trapped in crystals hop or tunnel?2 AbstractWater molecules trapped in crystals of barium chlorate monohydrate have been investigated by magic angle spinning proton NMR spectroscopy in the temperature range 110-300 K. At high temperatures, a single spinning sideband pattern is observed. Below 150 K however, two interleaved spinning sideband manifolds appear, with distinct centerbands that do not coincide with the average isotropic chemical shift seen at high temperatures. This hitherto unknown "cross-term splitting" results from the interplay of the homonuclear dipoledipole coupling and two anisotropic proton shielding tensors that have identical principal components but non-equivalent orientations. The resulting cross terms cannot be averaged out by rotation about the magic angle. The analysis of the exchange-induced broadening, coalescence and narrowing of the cross-term splitting in MAS spectra allows one to estimate the rate of exchange of the two protons between 140 and 190 K. The experimental data is compared with 2 H and 1 H NMR studies of the same sample reported in the literature. DFT methods are utilized to estimate the thermal activation energy for a two-fold hopping process of proton exchange about the H-O-H bisector. The Bell-Limbach model allows one to take into account contributions due to incoherent quantum tunneling in the low temperature regime.

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“…Such a method needs to account for the quantum nature of the nucleus system. Multi-component (MC) density-functional theory (DFT) [ 43 ] uses a full quantum-mechanical description of all or selected nuclei and has been used for example, to determine NMR isotopic shifts in aromatic hydroxy acyl compounds [ 44 ] Recently, NMR isotopic shifts were calculated incorporating nuclear quantum effects by path-integral molecular dynamics (PIMD) [ 45 , 46 , 47 ]. However, most calculations of NMR isotopic shifts start from the Born-Oppenheimer approximation [ 48 ] and scan potential-energy and property surfaces of the molecule around its equilibrium geometry.…”

Section: Introductionmentioning

confidence: 99%

The Structure of the “Vibration Hole” around an Isotopic Substitution—Implications for the Calculation of Nuclear Magnetic Resonance (NMR) Isotopic Shifts

Gräfenstein¹

2020

Molecules

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Calculations of nuclear magnetic resonance (NMR) isotopic shifts often rest on the unverified assumption that the “vibration hole”, that is, the change of the vibration motif upon an isotopic substitution, is strongly localized around the substitution site. Using our recently developed difference-dedicated (DD) second-order vibrational perturbation theory (VPT2) method, we test this assumption for a variety of molecules. The vibration hole turns out to be well localized in many cases but not in the interesting case where the H/D substitution site is involved in an intra-molecular hydrogen bond. For a series of salicylaldehyde derivatives recently studied by Hansen and co-workers (Molecules 2019, 24, 4533), the vibrational hole was found to stretch over the whole hydrogen-bond moiety, including the bonds to the neighbouring C atoms, and to be sensitive to substituent effects. We discuss consequences of this finding for the accurate calculation of NMR isotopic shifts and point out directions for the further improvement of our DD-VPT2 method.

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Proton transfer in guanine–cytosine base pair analogues studied by NMR spectroscopy and PIMD simulations

Cited by 34 publications

References 61 publications

Tautomerism of Guanine Analogues

Tautomerism of Guanine Analogues

Cross-term Splittings Due to the Orientational Inequivalence of Proton Magnetic Shielding Tensors: Do Water Molecules Trapped in Crystals Hop or Tunnel?

The Structure of the “Vibration Hole” around an Isotopic Substitution—Implications for the Calculation of Nuclear Magnetic Resonance (NMR) Isotopic Shifts

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