On the importance of nuclear quantum motions in near edge x-ray absorption fine structure spectroscopy of molecules

Schwartz, Craig P.; Uejio, Janel S.; Saykally, Richard J.

doi:10.1063/1.3125509

Cited by 40 publications

(64 citation statements)

References 39 publications

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“…We simulated the atomic configurations of triglycine with and without additional salts in aqueous solution at 300 K using classical molecular dynamics. Sampling a trajectory in our DFT simulation captures the impact of nuclear motion on the calculated spectrum (21). This technique has been used previously to interpret the spectra of solvated amino acids and the prototypical aromatic molecule, pyrrole in aqueous solutions (22,23).…”

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Investigation of protein conformation and interactions with salts via X-ray absorption spectroscopy

Schwartz

Uejio

Duffin

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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The authors note that the results of their article indicated that sulfite interacts more directly with the peptide than does bromide. These results do not refute nor contradict the work of Cremer and coworkers involving the interactions of anions with poly(N-isopropylacrylamide) (1). In the case of Cremer's work, a direct Hofmeister series is followed. For triglycine, however, at least a partially reversed Hofmeister series might be expected (2, 3), because this molecule contains a site of positive charge.

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confidence: 99%

Investigation of protein conformation and interactions with salts via X-ray absorption spectroscopy

Schwartz

Uejio

Duffin

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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“…Extensions which minimize the computational cost of this approach and also incorporate nuclear motions have been developed more recently and applied to the solvation of small organic molecules in water. 33,34 …”

Section: Methodsmentioning

confidence: 99%

Local Effects in the X-ray Absorption Spectrum of Salt Water

et al. 2010

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Both first-principles molecular dynamics and theoretical X-ray absorption spectroscopy have been used to investigate the aqueous solvation of cations in 0.5 M MgCl 2 , CaCl 2 , and NaCl solutions. We focus here on the species-specific effects that Mg 2+ , Ca 2+ , and Na + have on the X-ray absorption spectrum of the respective solutions. For the divalent cations, we find that the hydrogen-bonding characteristics of the more rigid magnesium first-shell water molecules differ from those in the more flexible solvation shell surrounding calcium. In particular, the first solvation shell water molecules of calcium are able to form acceptor hydrogen bonds, and this results in an enhancement of a post-edge peak near 540 eV. The absence of acceptor hydrogen bonds for magnesium first shell water molecules provides an explanation for the experimental and theoretical observation of a lack of enhancement at the post-main-edge peak. For the sodium monovalent cation we find that the broad tilt angle distribution results in a broadening of postedge features, despite populations in donorand-acceptor configurations consistent with calcium. We also present the reaveraged spectra of the MgCl 2 , CaCl 2 , and NaCl solutions and show that trends apparent with increasing concentration (0.5, 2.0, 4.0 M) are consistent with experiment. Finally, we examine more closely both the effect that cation coordination number has on the hydrogen-bonding network and the relative perturbation strength of the cations on lone pair oxygen orbitals.

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“…In all of our calculations, we use norm-conserving pseudopotentials with a numerically converged plane-wave cutoff of 85 Ry. We analyze the population of the bound states within the XCH approximation [10].…”

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“…We use the excited electron and core hole (XCH) method, already demonstrated to work well for molecular liquids. The XCH method models the associated excited states self-consistently, with the combination of a full electronic core hole on the excited atom and an excited electron, which significantly screens the core hole in molecular systems [9,10]. Our electronic structure calculations employed density functional theory using the PerdewBurke-Ernzerhof (PBE) functional theory using the Perdew-Burke-Ernzerhof (PBE) form of the generalized gradient approximation to the exchange-correlation potential [11].…”

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Importance of Electronic Relaxation for Inter-Coulombic Decay in Aqueous Systems

2010

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Inspired by recent photoelectron spectroscopy experiments on hydroxide solutions, we have examined the conditions necessary for enhanced (and, in the case of solutions, detectable) inter-Coulombic decay (ICD)-Auger emission from an atomic site other than that originally excited. We present general guidelines, based on energetic and spatial overlap of molecular orbitals, for this enhancement of inter-Coulombic decay-based energy transfer in solutions. These guidelines indicate that this decay process should be exhibited by broad classes of biomolecules and suggest a design criterion for targeted radiooncology protocols. Our findings show that photoelectron spectroscopy cannot resolve the current hydroxide coordination controversy.An Auger process (see Fig. 1) involves the decay of a photo-excited electron-hole pair via annihilation of the hole by another electron, with simultaneous emission of an electron from a bound state to the continuum [1]. The rate is governed (in a Fermi golden rule framework) by both direct and exchange Coulomb integrals [2]. For photo-excited holes in inner-valence or core states, the associated orbitals are well localized on a given atom, such that Auger spectra are typically dominated by atom-specific transitions. Atomic and molecular phases comprise mainly localized electronic orbitals, and the decay rate is consequently quite small for processes involving electron emission from any atomic site other than that originally excited. In such systems, this type of ''off-site'' emission has been labeled as ICD, inter-Coulombic (atomic or molecular) decay [3].Although ICD has been studied primarily in the context of valence excitations [3][4][5], recent experiments have shown that core-excited systems may also decay in this fashion, as shown schematically in Fig. 1 [6]. Panel (a) depicts the instantaneous ground-state potential landscape and electron configuration for two atoms separated by some distance. The core electrons have energy substantially lower than the valence electrons and are tightly bound to the atomic nucleus, screening the nuclear charge Z such that the valence electrons are subject to an effective nuclear Coulomb potential proportional to Zeff ¼ Z _ 2, consistent with Gauss's law. (For the purpose of this discussion, we assume that A and B are atoms of first-row elements with 1s core electrons only.) These effective potentials, when added together, give rise to the multiple-Coulombwell landscape shown in Fig. 1(a), which will support some localized bound states and additional bonding states spanning multiple atomic centers. Core excitation of a given atom [ Fig. 1(b)] will increment the effective nuclear charge, steepening the local potential landscape at that site. This will cause a sudden downward shift in the energy of some electronic states, which in some cases may prevent coupling with states from neighboring atomic sites, or in others may lead to new electronic hybridization via tunneling through the resulting potential barrier. The key point for the present work is t...

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On the importance of nuclear quantum motions in near edge x-ray absorption fine structure spectroscopy of molecules

Cited by 40 publications

References 39 publications

Investigation of protein conformation and interactions with salts via X-ray absorption spectroscopy

Investigation of protein conformation and interactions with salts via X-ray absorption spectroscopy

Local Effects in the X-ray Absorption Spectrum of Salt Water

Importance of Electronic Relaxation for Inter-Coulombic Decay in Aqueous Systems

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