Mineral–Water Interaction

Gaigeot, Marie‐Pierre; Sulpizi, Marialore

doi:10.1002/9781118845226.ch8

Cited by 8 publications

(5 citation statements)

References 178 publications

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“…Besides predicting crystal structures and elastic behaviour of geochemical systems (Kubicki 2016), simulations may guide experiments by providing atomistic insight often difficult to access in a laboratory (Marx and Hutter 2009;Tabacchi et al 2014b;Van Speybroeck et al 2015;Gaigeot and Sulpizi 2016). Theoretical techniques are particularly valuable at the temperature and pressure conditions typical of earth's mantle or extra-terrestrial environments (Cruciani 2006;Liang et al 2007), where experimental observation is often unfeasible (Gatta et al 2018;Kong et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Computer modeling of apparently straight bond angles: The intriguing case of all-silica ferrierite

Trudu

Tabacchi

Fois

2019

American Mineralogist

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The relationships between synthetic zeolites and their natural counterparts that have been unveiled by theoretical studies have contributed to improving the properties and applications of zeolite-based materials in strategic areas such as industrial catalysis, environmental protection, and solar energy harvesting. To pinpoint the role of modeling in zeolite science, we discuss an example of computationally driven problem solving: can tetrahedral frameworks sustain straight (i.e., 180°) Si-O-Si bond angles? The true crystal symmetry of zeolite ferrierite (FER), especially in its all-silica form, had been intensely debated for 30 years before being solved in the Pmnn space group. Yet there are indications that an Immm structure with energetically unfavorable linear Si-O-Si linkages could be formed at high temperature. To gather insight, we perform density functional theory (DFT) optimizations and frequency calculations of all-silica ferrierite in both the Pmnn and Immm space groups. Our results indicate that Pmnn is more stable than Immm, in line with experiments. While the Pmnn structure is a true minimum in the energy profile of ferrierite, the Immm structure has four imaginary frequency vibrations, three of which are localized on the 180° Si-O-Si angles. This suggests that ferrierites with Immm symmetry may be classified as metastable phases. Such a designation is also supported by first-principles molecular dynamics on Immm FER, showing that the average value of 180° actually results from Si-O-Si angle inversion. An implication of this study with interesting geological and technological consequences is the association of straight Si-O-Si angles experimentally detected in open-framework or low-density silicates to an angle-inversion process occurring at the femtosecond scale. Such flexibility of the apparently flat Si-O-Si linkages might play an important role in sorption phenomena, which are ubiquitous in geological processes and industrial applications alike.

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Section: Introductionmentioning

confidence: 99%

Computer modeling of apparently straight bond angles: The intriguing case of all-silica ferrierite

Trudu

Tabacchi

Fois

2019

American Mineralogist

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“…The latter method, which is adopted to exploret he influence of finite temperature and conformational dynamics of the presentlyi nvestigated flexible species, allows anharmonic effects to be directly included in the spectroscopica nalysis and vibrational transitions to be adequately interpreted. [48,49] It needs to be underlined that the adopted [cysSO x ] À notation does not indicate the actual deprotonation site, which may be either the SO x Ho rt he carboxylic group, but simply labels the investigated speciesb yi ndicating the number of Sbondedo xygen atoms.…”

Section: Introductionmentioning

confidence: 99%

Amino Acid Oxidation: A Combined Study of Cysteine Oxo Forms by IRMPD Spectroscopy and Simulations

Scuderi

Bodo

Chiavarino

et al. 2016

Chemistry A European J

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The redox activity of cysteine sulfur allows numerous post-translational protein modifications involved in the oxidative regulation of metabolism, in metal binding, and in signal transduction. A combined approach based on infrared multiple photon dissociation spectroscopy at the Centre Laser Infrarouge d'Orsay (CLIO) free electron laser facility, calculations of IR frequencies, and finite temperature ab initio molecular dynamics simulations has been employed to characterize the gas-phase structures of deprotonated cysteine sulfenic, sulfinic, and sulfonic acids, [cysSO ] (x=1, 2, 3, representing the number of S-bound oxygen atoms), which are key intermediates in the redox-switching chemistry of proteins. The ions show different structural motifs owing to preferential binding of the proton to either the carboxylate or sulfur-containing group. Due to the decreasing basicity of the sulfenic, sulfinic, and sulfonic terminals, the proton bound to SO in [cysSO] migrates to the carboxylate in [cysSO ] , whereas it turns out to be shared in [cysSO ] . Evidence is gathered that a mixture of close-lying low-energy conformers is sampled for each cysteine oxo form in a Paul ion trap at room temperature.

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“…Below, VDOS curves will be computed by using AIMD based on periodic DFT, for canonical (finite temperature) ensembles of the systems under study. Classical molecular dynamics trajectories can provide direct access to vibrational spectra such as IR and VSF, employing other correlation functions according to linear response theory, 20,34,[37][38][39][40][41][42][43][44] where mode intensities and selection rules are properly taken into account. An IR spectrum is related to the first-order optical susceptibility, χ (1) , which can be calculated from the Fourier transform of the dipole-dipole autocorrelation function,…”

Section: Computation Of Vibrational Spectra: Methodsmentioning

confidence: 99%

Vibrational spectra of dissociatively adsorbed D2O on Al-terminated α-Al2O3(0001) surfaces from ab initio molecular dynamics

Melani

Nagata

Campen

et al. 2019

The Journal of Chemical Physics

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Mineral–Water Interaction

Cited by 8 publications

References 178 publications

Computer modeling of apparently straight bond angles: The intriguing case of all-silica ferrierite

Computer modeling of apparently straight bond angles: The intriguing case of all-silica ferrierite

Amino Acid Oxidation: A Combined Study of Cysteine Oxo Forms by IRMPD Spectroscopy and Simulations

Vibrational spectra of dissociatively adsorbed D2O on Al-terminated α-Al2O3(0001) surfaces from ab initio molecular dynamics

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