Size-dependent proton localization in hydrated uracil clusters: A joint experimental and theoretical study

Abstract

A collision-induced dissociation study of hydrated protonated uracil (H 2 O) n=1-15 UH + clusters is reported. The mass-selected clusters collide with water molecules and rare gases at a controlled center of mass collision energy. From these measurements, absolute fragmentation cross sections and branching ratios are extracted as a function of the uracil hydration. For small clusters, up to n = 4, we observe that only neutral water molecules are evaporated upon collisions, whereas for larger clusters neutral uracil is also evaporated: this transition in the nature of the evaporation products is interpreted considering the lowest-energy isomers of each species that are obtained from a combination of density-functional based tight-binding (DFTB) and MP2 calculations. The simulations show that in (H 2 O) 1-4 UH + the proton is located on the uracil molecule or on a water molecule strongly bound to uracil whereas, in larger clusters, the proton is bound to water molecules far from uracil. This correlation between the structure of the low-energy isomers and the experimental fragmentation channel suggests that dissociation may occur in a very short time after collisions, so that energy has not enough time to be redistributed among all degrees of freedom and the ground-state geometry of the parent cluster partly determines the nature of the favored fragmentation channels. Of course, thermal dissociations originating from long lived, thus thermalized, collision complexes cannot be ruled out but they are not expected to play the major role since experimental results can be satisfactorily accounted for by assuming that the fragmentation processes are mainly impulsive.

Non-ergodic fragmentation upon collision-induced activation of cysteine–water cluster cations

“… 93 More recently, “impulsive” dissociation was used to describe uracil–water cluster ion dissociation upon collisions with 7.2 eV Ne atoms indicating rather common occurrence of this mechanism in the collision activation process. 87,94 We conclude that non-ergodic loss of a single water molecule represents the most plausible explanation of the high intensity of this reaction channel in the present experiment. Since the “ergodic” peak in the fitted energy distributions ( Fig.…”

“…The thiol thiolate change has a significant role in the biochemistry of cysteine, but we can see that in the present case of small water clusters it has practically no influence on the binding of water to the central cation. However, demonstrated by several recent theoretical and experimental studies of microhydrated nucleobases, [86][87][88] the microhydrated environment does not necessarily resemble that of a bulk water.…”

Diversity of protonated mixed pyrene–water clusters investigated by collision induced dissociation

“…In a previous examination of protonated hydrated uracil clusters, we determined that the observed experimental fragmentation channels were indicative of the low-energy isomers' structure, emphasizing the CID method's utility in probing source-formed isomer structures. 27,28 In this study, we identify different isomers of protonated pyrene-water complexes and discuss their structures using results from density functional theory. We also pinpoint preferred formation conditions triggered by ionized seeds, including protonated pyrene, and discuss potential astrophysical implications.…”