Imaging the Translational Dynamics of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mrow><mml:mi mathvariant="normal">C</mml:mi><mml:mi mathvariant="normal">F</mml:mi></mml:mrow><mml:mn>3</mml:mn></mml:msub></mml:math>in Liquid Helium Droplets

Braun, A.; Drabbels, Marcel

doi:10.1103/physrevlett.93.253401

Cited by 51 publications

(47 citation statements)

References 29 publications

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“…At variance with previous studies [11,12,13], here we exploit two independent methods: one based on an extended version of the Jarzynski equality (EJE) and the other on thermodynamical averages over ISs. Moreover, the agreement of the results obtained with the two approaches indicates that these two methodologies can be fruitfully integrated to provide complementary information on the protein landscape.…”

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Reconstructing the Free-Energy Landscape of a Mechanically Unfolded Model Protein

2007

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The equilibrium free energy landscape of an off-lattice model protein as a function of an internal (reaction) coordinate is reconstructed from out-of-equilibrium mechanical unfolding manipulations. This task is accomplished via two independent methods: by employing an extended version of the Jarzynski equality (EJE) and the protein inherent structures (ISs). In a range of temperatures around the "folding transition" we find a good quantitative agreement between the free energies obtained via EJE and IS approaches. This indicates that the two methodologies are consistent and able to reproduce equilibrium properties of the examined system. Moreover, for the studied model the structural transitions induced by pulling can be related to thermodynamical aspects of folding.PACS numbers: 87.15. Aa,82.37.Rs,05.90.+m The properties of the (free) energy landscape can heavily influence the dynamical and thermodynamical features of a large class of systems: supercooled liquids, glasses, atomic clusters and biomolecules [1]. In particular, the shape of the landscape plays a major role in determining the folding properties of proteins [2]. A fruitful approach to the analysis of the landscape relies on the identification of the local minima of the potential energy, i.e. the "inherent structures" (ISs) of the system [3]. The investigation of the ISs has lead to the identification of the structural-arrest temperature in glasses [4] and supercooled liquids [5]. More recently, this kind of analysis has been extended to the study of proteins [6,7].Mechanical unfolding of single biomolecules represents a powerful technique to extract information on their internal structure as well as on their unfolding and refolding pathways [8]. However, mechanical unfolding of biomolecules is an out-of-equilibrium process: unfolding events occur on time scales much shorter than the typical relaxation time of the molecule towards equilibrium. Nonetheless, by using the equality introduced by Jarzynski [9], the free energy of mechanically manipulated biomolecules can be recovered as a function of an externally controlled parameter [10].In this Letter, we reconstruct the equilibrium free energy landscape (FEL) associated to a mesoscopic offlattice protein model as a function of an internal coordinate of the system (namely, the end-to-end distance ζ). At variance with previous studies [11,12,13], here we exploit two independent methods: one based on an extended version of the Jarzynski equality (EJE) and the other on thermodynamical averages over ISs. Moreover, the agreement of the results obtained with the two approaches indicates that these two methodologies can be fruitfully integrated to provide complementary information on the protein landscape. In particular the investigation of the ISs allows us to give an estimate of the (free) energetic and entropic barriers separating the native state from the completely stretched configuration.The model studied in this paper is a modified version of the 3d off-lattice model introduced in Ref. [14] and succ...

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Reconstructing the Free-Energy Landscape of a Mechanically Unfolded Model Protein

2007

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“…The experimental results of Braun and Drabbels were simulated successfully by this procedure. 12 We have used the same simulation program to examine our data.…”

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“…11 A recent study created moving neutral impurities within the droplet with well-defined kinetic energy and gave direct evidence of translational energy dissipation in the droplet. 12 The above experiments were conducted with neutral impurities, where the interaction between the dopant and surrounding helium is expected to be weak. With ions, the situation may be different.…”

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confidence: 99%

Photoionization and Photofragmentation of SF₆in Helium Nanodroplets

et al. 2006

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The photoionization of He droplets doped with SF 6 was investigated using tunable vacuum ultraviolet (VUV) synchrotron radiation from the Advanced Light Source (ALS). The resulting ionization and photofragmentation dynamics were characterized using time-of-flight mass spectrometry combined with photofragment and photoelectron imaging. Results are compared to those of gas-phase SF 6 molecules. We find dissociative photoionization to SF 5 + to be the dominant channel, in agreement with previous results. Key new findings are that (a) the photoelectron spectrum of the SF 6 in the droplet is similar but not identical to that of the gas-phase species, (b) the SF 5 + photofragment velocity distribution is considerably slower upon droplet photoionization, and (c) fragmentation to SF 4 + and SF 3 + is much less than in the photoionization of bare SF 6 . From these measurements we obtain new insights into the mechanism of SF 6 photoionization within the droplet and the cooling of the hot photofragment ions produced by dissociative photoionization.

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“…In a photoionization experiment, Braun and Drabbels used UV light at 266 nm to ionize a CF 3 I molecule embedded in the helium nanodroplet. 12 They found that the neutral CF 3 4 fragment escapes via a direct mechanism, and only partially transfers its excess kinetic energy to helium nanodroplets. Fárník and Toennies investigated the ionization of binary molecular clusters of N 2 /D 2 and CH 4 /D 2 and found that ionization of molecular clusters in helium droplets starts with charge transfer reactions between He + and one of the dopant molecules, followed by secondary reactions between the primary charge transfer products and the remaining neutral molecules.…”

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confidence: 99%

Role of Helium Droplets in Mass Spectra of Diatomics: Suppression of Dissociative Reactions

Ellis

Yang

2015

Chinese Journal of Chemical Physics

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It is generally accepted that electron impact of doped helium nanodroplets initially produces a positively charged helium atom, which then ionizes the dopant if the two come into contact. In effect the He + can initiate ion-molecule reactions. However, the effect of the surrounding helium on ion-molecule reactions remains ambiguous. To explore this, electron-induced chemistry has been investigated for the diatomic molecules O 2 , CO and N 2 . The helium is found to significantly suppress dissociative ion product channels.3

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Imaging the Translational Dynamics ofCF3in Liquid Helium Droplets

Cited by 51 publications

References 29 publications

Reconstructing the Free-Energy Landscape of a Mechanically Unfolded Model Protein

Reconstructing the Free-Energy Landscape of a Mechanically Unfolded Model Protein

Photoionization and Photofragmentation of SF₆in Helium Nanodroplets

Role of Helium Droplets in Mass Spectra of Diatomics: Suppression of Dissociative Reactions

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Imaging the Translational Dynamics ofCF3in Liquid Helium Droplets

Cited by 51 publications

References 29 publications

Reconstructing the Free-Energy Landscape of a Mechanically Unfolded Model Protein

Reconstructing the Free-Energy Landscape of a Mechanically Unfolded Model Protein

Photoionization and Photofragmentation of SF6in Helium Nanodroplets

Role of Helium Droplets in Mass Spectra of Diatomics: Suppression of Dissociative Reactions

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Photoionization and Photofragmentation of SF₆in Helium Nanodroplets