A DFT study of uracil and 5-bromouracil in nanodroplets

Mourik, Tanja van; Danilov, V.I.; Dailidonis, Vladimir V.; Kurita, Noriyuki; Wakabayashi, Hajime; Tsukamoto, Takayuki

doi:10.1007/s00214-009-0630-0

Cited by 31 publications

(14 citation statements)

References 75 publications

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“…The 5X‐uracils with X = F, Cl, Br, or I are employed to increase the sensitivity of DNA against ionising radiation and play roles in cancer treatment. 5‐Bromouracil is a known mutagen; the last years our group has been interested in the mutagenic mechanism of this base, including the role of hydration . Ho et al have shown that a halogen bond formed between a brominated uracil and an oxygen on a phosphate group can be engineered to direct the conformation of a DNA Holliday junction .…”

Section: Introductionmentioning

confidence: 99%

Competition between hydrogen and halogen bonding in halogenated 1‐methyluracil: Water systems

Hogan

Mourik

2016

J Comput Chem

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The competition between hydrogen‐ and halogen‐bonding interactions in complexes of 5‐halogenated 1‐methyluracil (XmU; X = F, Cl, Br, I, or At) with one or two water molecules in the binding region between C5‐X and C4O4 is investigated with M06‐2X/6‐31+G(d). In the singly‐hydrated systems, the water molecule forms a hydrogen bond with C4O4 for all halogens, whereas structures with a halogen bond between the water oxygen and C5‐X exist only for X = Br, I, and At. Structures with two waters forming a bridge between C4O and C5‐X (through hydrogen‐ and halogen‐bonding interactions) exist for all halogens except F. The absence of a halogen‐bonded structure in singly‐hydrated ClmU is therefore attributed to the competing hydrogen‐bonding interaction with C4O4. The halogen‐bond angle in the doubly‐hydrated structures (150–160°) is far from the expected linearity of halogen bonds, indicating that significantly non‐linear halogen bonds may exist in complex environments with competing interactions. © 2016 Wiley Periodicals, Inc.

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Section: Introductionmentioning

confidence: 99%

Competition between hydrogen and halogen bonding in halogenated 1‐methyluracil: Water systems

Hogan

Mourik

2016

J Comput Chem

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“…They used M05-2X and a functional including molecular mechanics terms to verify the structure and relative stabilities of the 20 most stable conformers. van Mourik et al [205] used M05-2X and B3LYP to study the keto and enol tautomers of uracil and 5-bromouracil in nanodroplets of up to 100 water molecules.…”

Section: Biological and Medicinal Chemistrymentioning

confidence: 99%

Applications and validations of the Minnesota density functionals

Zhao

Truhlar

2011

Chemical Physics Letters

696

329

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“…Whereas various theoretical studies have been carried out on uracil-water clusters, [41][42][43][44][45][46] experimental studies are scarce. The present work provides the first MPI mass spectrum of uracil-water clusters.…”

Section: Hydrated Clustersmentioning

confidence: 99%

Multi-photon ionization and fragmentation of uracil: Neutral excited-state ring opening and hydration effects

Barc

Ryszka

Spurrell

et al. 2013

The Journal of Chemical Physics

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Multi-photon ionization (MPI) of the RNA base uracil has been studied in the wavelength range 220–270 nm, coinciding with excitation to the S2(ππ*) state. A fragment ion at m/z = 84 was produced by 2-photon absorption at wavelengths ≤232 nm and assigned to C3H4N2O+ following CO abstraction. This ion has not been observed in alternative dissociative ionization processes (notably electron impact) and its threshold is close to recent calculations of the minimum activation energy for a ring opening conical intersection to a σ(n-π)π* closed shell state. Moreover, the predicted ring opening transition leaves a CO group at one end of the isomer, apparently vulnerable to abstraction. An MPI mass spectrum of uracil-water clusters is presented for the first time and compared with an equivalent dry measurement. Hydration enhances certain fragment ion pathways (particularly C3H3NO+) but represses C3H4N2O+ production. This indicates that hydrogen bonding to water stabilizes uracil with respect to neutral excited-state ring opening.

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A DFT study of uracil and 5-bromouracil in nanodroplets

Cited by 31 publications

References 75 publications

Competition between hydrogen and halogen bonding in halogenated 1‐methyluracil: Water systems

Competition between hydrogen and halogen bonding in halogenated 1‐methyluracil: Water systems

Applications and validations of the Minnesota density functionals

Multi-photon ionization and fragmentation of uracil: Neutral excited-state ring opening and hydration effects

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