Nature of Large Temporal Fluctuations of Hydrogen Transfer Rates in Single Molecules

Piątkowski, Łukasz; Schanbacher, Christina; Wackenhut, Frank; Jamrozik, Agnieszka; Meixner, Alfred J.; Waluk, Jacek

doi:10.1021/acs.jpclett.8b00299

Cited by 22 publications

(26 citation statements)

References 40 publications

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“…Direct comparison between our gas-phase calculation and these results in certain condensed-phase environments is supported by the observation of negligible solvent dependency in experiments. 40,41 In other types of environments such as surfaces 42,43 or polymer matrices, 44 the rate depends more strongly on the environment. Larger porphycene derivatives show rate dependency in both isotropic 41 and non-isotropic environments.…”

Section: Results and Discussionmentioning

confidence: 99%

Elucidating the Nuclear Quantum Dynamics of Intramolecular Double Hydrogen Transfer in Porphycene

et al. 2019

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We address the double hydrogen transfer (DHT) dynamics of the porphycene molecule, a complex paradigmatic system in which the making and breaking of H-bonds in a highly anharmonic potential energy surface require a quantum mechanical treatment not only of the electrons but also of the nuclei. We combine density functional theory calculations, employing hybrid functionals and van der Waals corrections, with recently proposed and optimized path-integral ring-polymer methods for the approximation of quantum vibrational spectra and reaction rates. Our full-dimensional ring-polymer instanton simulations show that below 100 K the concerted DHT tunneling pathway dominates but between 100 and 300 K there is a competition between concerted and stepwise pathways when nuclear quantum effects are included. We obtain ground-state reaction rates of 2.19 × 10 11 s –1 at 150 K and 0.63 × 10 11 s –1 at 100 K, in good agreement with experiment. We also reproduce the puzzling N–H stretching band of porphycene with very good accuracy from thermostated ring-polymer molecular dynamics simulations. The position and line shape of this peak, centered at around 2600 cm –1 and spanning 750 cm –1 , stem from a combination of very strong H-bonds, the coupling to low-frequency modes, and the access to cis -like isomeric conformations, which cannot be appropriately captured with classical-nuclei dynamics. These results verify the appropriateness of our general theoretical approach and provide a framework for a deeper physical understanding of hydrogen transfer dynamics in complex systems.

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Section: Results and Discussionmentioning

confidence: 99%

Elucidating the Nuclear Quantum Dynamics of Intramolecular Double Hydrogen Transfer in Porphycene

et al. 2019

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“…PT reactions occur via transition state (TS) (Hratchian and Schlegel, 2005) with one imaginary frequency connecting the reagent and product at the PES. Then, the reaction proceeds over or under the barrier via the tunneling (Löwdin, 1963; Bell, 1980; Koch et al, 2017; Piatkowski et al, 2018; Smedarchina et al, 2018). At this stage, the energy level of proton is equal for the reactants and products (Li et al, 2011; Ceriotti et al, 2016).…”

Section: Proton Transfer In Nucleobasesmentioning

confidence: 99%

The Role of Proton Transfer on Mutations

Srivastava

2019

Front. Chem.

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Hydrogen bonds play a critical role in nucleobase studies as they encode genes, map protein structures, provide stability to the base pairs, and are involved in spontaneous and induced mutations. Proton transfer mechanism is a critical phenomenon that is related to the acid–base characteristics of the nucleobases in Watson–Crick base pairs. The energetic and dynamical behavior of the proton can be depicted from these characteristics and their adjustment to the water molecules or the surrounding ions. Further, new pathways open up in which protonated nucleobases are generated by proton transfer from the ionized water molecules and elimination of a hydroxyl radical in this review, the analysis will be focused on understanding the mechanism of untargeted mutations in canonical, wobble, Hoogsteen pairs, and mutagenic tautomers through the non-covalent interactions. Further, rare tautomer formation through the single proton transfer (SPT) and the double proton transfer (DPT), quantum tunneling in nucleobases, radiation-induced bystander effects, role of water in proton transfer (PT) reactions, PT in anticancer drugs–DNA interaction, displacement and oriental polarization, possible models for mutations in DNA, genome instability, and role of proton transfer using kinetic parameters for RNA will be discussed.

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“…However, a major challenge to study tautomerization is that individual tautomeric species often cannot be isolated [ 9 ] and single‐molecule spectroscopy and theoretical studies are used to overcome this difficulty. Single‐molecule spectroscopy/microscopy has the major advantage that it avoids ensemble averaging and hence allows to observe processes, such as diffusion, [ 18 ] spectral diffusion, [ 19,20 ] or intramolecular proton transfer, [ 21 ] which are hidden in a classical ensemble experiment. Similarly, single‐molecule experiments enable to study conformational transitions and tautomerization of hypericin, a molecule which can be found in nature in Hypericum perforatum (St. John's wort).…”

Section: Introductionmentioning

confidence: 99%

Theoretical and Experimental Evidence of Two‐Step Tautomerization in Hypericin

Liu

Wang

Roldao

et al. 2021

Advanced Photonics Research

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Hypericin has large potential in modern medicine and exhibits fascinating structural dynamics, such as multiple conformations and tautomerization. However, it is difficult to study individual conformers/tautomers, as they cannot be isolated due to the similarity of their chemical and physical properties. An approach to overcome this difficulty is to combine single molecule experiments with theoretical studies. Time‐dependent density functional theory (TD‐DFT) calculations reveal that tautomerization of hypericin occurs via a two‐step proton transfer with an energy barrier of 1.63 eV, whereas a direct single‐step pathway has a large activation energy barrier of 2.42 eV. Tautomerization in hypericin is accompanied by reorientation of the transition dipole moment, which can be directly observed by fluorescence intensity fluctuations. Quantitative tautomerization residence times can be obtained from the autocorrelation of the temporal emission behavior revealing that hypericin stays in the same tautomeric state for several seconds, which can be influenced by the embedding matrix. Furthermore, replacing hydrogen with deuterium further proves that the underlying process is based on tunneling of a proton. In addition, the tautomerization rate can be influenced by a λ/2 Fabry–Pérot microcavity, where the occupation of Raman active vibrations can alter the tunneling rate.

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Nature of Large Temporal Fluctuations of Hydrogen Transfer Rates in Single Molecules

Cited by 22 publications

References 40 publications

Elucidating the Nuclear Quantum Dynamics of Intramolecular Double Hydrogen Transfer in Porphycene

Elucidating the Nuclear Quantum Dynamics of Intramolecular Double Hydrogen Transfer in Porphycene

The Role of Proton Transfer on Mutations

Theoretical and Experimental Evidence of Two‐Step Tautomerization in Hypericin

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