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De Francesco A, Formisano F, Scaccia L, Guarini E, Bafile U, González MA, Alatas A, Lynch ST, Cunsolo A. Fingerprints of hydrogen bonding in the terahertz dynamics of ethanol and water: An inelastic x-ray scattering study. J Chem Phys 2023; 159:244501. [PMID: 38131485 DOI: 10.1063/5.0180961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
We used inelastic x-ray scattering methods to measure the terahertz spectrum of density fluctuations of ethanol in both liquid and solid phases. The results of a Bayesian inference-based lineshape analysis with a multiple excitation model and the comparison with a previous similar analysis on water indicate that the different structures induced by hydrogen bonds in ethanol and water have a profound influence on the respective dynamic responses, the latter being characterized by longer living and better resolved high-frequency acoustic excitations. In addition, we compare these findings with those obtained with an alternative approach based on the exponential expansion theory and ensuring sum rules fulfillment, demonstrating that the model's choice directly impacts the number of spectral modes detected.
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Affiliation(s)
- A De Francesco
- CNR-IOM and INSIDE@ILL c/o Operative Group in Grenoble (OGG), F-38042 and Institut Laue Langevin, F-38042 Grenoble, France
| | - F Formisano
- CNR-IOM and INSIDE@ILL c/o Operative Group in Grenoble (OGG), F-38042 and Institut Laue Langevin, F-38042 Grenoble, France
| | - L Scaccia
- Dipartimento di Economia e Diritto, Università di Macerata, via Crescimbeni 20, 62100 Macerata, Italy
| | - E Guarini
- Dipartimento di Fisica e Astronomia, Università di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino, Italy
| | - U Bafile
- Consiglio Nazionale delle Ricerche, Istituto di Fisica Applicata "Nello Carrara", via Madonna del Piano 10, I-50019 Sesto Fiorentino, Italy
| | - M A González
- Institut Laue Langevin, 72 Avenue des Martyrs, F-38042 Grenoble, France
| | - A Alatas
- Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - S T Lynch
- Department of Physics, University of Wisconsin-Madison, 1150 University Avenue, Madison, Wisconsin 53706, USA
| | - A Cunsolo
- Department of Physics, University of Wisconsin-Madison, 1150 University Avenue, Madison, Wisconsin 53706, USA
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2
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Guarini E, Neumann M, De Francesco A, Formisano F, Cunsolo A, Montfrooij W, Colognesi D, Bafile U. Onset of collective excitations in the transverse dynamics of simple fluids. Phys Rev E 2023; 107:014139. [PMID: 36797969 DOI: 10.1103/physreve.107.014139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 01/10/2023] [Indexed: 06/18/2023]
Abstract
A thorough analysis of the transverse current autocorrelation function obtained by molecular dynamics simulations of a dense Lennard-Jones fluid reveals that even such a simple system is characterized by a varied dynamical behavior with changing length scale. By using the exponential expansion theory, we provide a full account of the time correlation at wavevectors Q between the upper boundary of the hydrodynamic region and Q_{p}/2, with Q_{p} being the position of the main peak of the static structure factor. In the Q range studied, we identify and accurately locate the wavevector at which shear wave propagation starts to take place, and show clearly how this phenomenon may be represented by a damped harmonic oscillator changing, in a continuous way, from an overdamped to an underdamped condition. The decomposition into exponential modes allows one to convincingly establish not only the crossover related to the onset of transverse waves but, surprisingly, also the existence of a second pair of modes equivalent to another oscillator that undergoes, at higher Q values, a similarly smooth over to underdamped transition.
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Affiliation(s)
- Eleonora Guarini
- Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino, Italy
| | - Martin Neumann
- Fakultät für Physik der Universität Wien, Kolingasse 14-16, A-1090 Wien, Austria
| | - Alessio De Francesco
- CNR-IOM & INSIDE@ILL c/o Operative Group in Grenoble (OGG) F-38042 Grenoble, France and Institut Laue Langevin (ILL), F-38042 Grenoble, France
| | - Ferdinando Formisano
- CNR-IOM & INSIDE@ILL c/o Operative Group in Grenoble (OGG) F-38042 Grenoble, France and Institut Laue Langevin (ILL), F-38042 Grenoble, France
| | - Alessandro Cunsolo
- Department of Physics, University of Wisconsin at Madison, 1150 University Avenue, Madison, Wisconsin 53706, United States
| | - Wouter Montfrooij
- Department of Physics and Astronomy, University of Missouri, Columbia, Missouri 65211, United States
| | - Daniele Colognesi
- Consiglio Nazionale delle Ricerche, Istituto di Fisica Applicata "Nello Carrara", via Madonna del Piano 10, I-50019 Sesto Fiorentino, Italy
| | - Ubaldo Bafile
- Consiglio Nazionale delle Ricerche, Istituto di Fisica Applicata "Nello Carrara", via Madonna del Piano 10, I-50019 Sesto Fiorentino, Italy
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3
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MD studies of methanol confined in the metal-organic framework MOF MIL-88B-Cl. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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4
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Hammerle F, Steger LM, Zhou X, Bonnet S, Huymann L, Peintner U, Siewert B. Optimized isolation of 7,7'-biphyscion starting from Cortinarius rubrophyllus, a chemically unexplored fungal species rich in photosensitizers. Photochem Photobiol Sci 2022; 21:221-234. [PMID: 34971447 PMCID: PMC8863709 DOI: 10.1007/s43630-021-00159-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/14/2021] [Indexed: 11/01/2022]
Abstract
Mushrooms such as the dermocyboid Cortinarius rubrophyllus are characterized by strikingly colorful fruiting bodies. The molecular dyes responsible for such colors recently experienced a comeback as photoactive compounds with remarkable photophysical and photobiological properties. One of them-7,7'-biphyscion-is a dimeric anthraquinone that showed promising anticancer effects in the low nanomolar range under blue-light irradiation. Compared to acidic anthraquinones, 7,7'-biphyscion was more efficiently taken up by cells and induced apoptosis after photoactivation. However, seasonal collection of mushrooms producing this compound, low extraction yields, and tricky fungal identification hamper further developments to the clinics. To bypass these limitations, we demonstrate here an alternative approach utilizing a precursor of 7,7'-biphyscion, i.e., the pre-anthraquinone flavomannin-6,6'-dimethyl ether, which is abundant in many species of the subgenus Dermocybe. Controlled oxidation of the crude extract significantly increased the yield of 7,7'-biphyscion by 100%, which eased the isolation process. We also present the mycochemical and photobiological characterization of the yet chemically undescribed species, i.e. C. rubrophyllus. In total, eight pigments (1-8) were isolated, including two new glycosylated anthraquinones (1 and 2). Light-dependent generation of singlet oxygen was detected for the first time for emodin-1-O-β-D-glucopyranoside (3) [photophysical measurement: Φ∆ = 0.11 (CD3OD)]. Furthermore, emodin (7) was characterized as promising compound in the photocytotoxicity assay with EC50-values in the low micromolar range under irradiation against cells of the cancer cell lines AGS, A549, and T24.
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Affiliation(s)
- Fabian Hammerle
- Pharmacology and Pharmacognosy, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Lisa-Maria Steger
- Pharmacology and Pharmacognosy, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Xuequan Zhou
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P.O Box 9502, 2300 RA, Leiden, The Netherlands
| | - Sylvestre Bonnet
- Gorlaeus Laboratories, Leiden Institute of Chemistry, Leiden University, P.O Box 9502, 2300 RA, Leiden, The Netherlands
| | - Lesley Huymann
- University of Innsbruck, Microbiology, Technikerstraße 25, 6020, Innsbruck, Austria
| | - Ursula Peintner
- University of Innsbruck, Microbiology, Technikerstraße 25, 6020, Innsbruck, Austria
| | - Bianka Siewert
- Pharmacology and Pharmacognosy, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
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5
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Alvarez F, Arbe A, Colmenero J. Unraveling the coherent dynamic structure factor of liquid water at the mesoscale by molecular dynamics simulations. J Chem Phys 2021; 155:244509. [PMID: 34972354 DOI: 10.1063/5.0074588] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present an investigation by molecular dynamics (MD)-simulations of the coherent dynamic structure factor, S(Q, t) (Q: momentum transfer), of liquid water at the mesoscale (0.1 Å-1 ≤ Q ≤ Qmax) [Qmax ≈ 2 Å-1: Q-value of the first maximum of the static structure factor, S(Q), of water]. The simulation cell-large enough to address the collective properties at the mesoscale-is validated by direct comparison with recent results on the dynamic structure factor in the frequency domain obtained by neutron spectroscopy with polarization analysis [Arbe et al., Phys. Rev. Res. 2, 022015 (2020)]. We have not only focused on the acoustic excitations but also on the relaxational contributions to S(Q, t). The analysis of the MD-simulation results-including the self- and distinct contributions to the diffusive part of S(Q, t)-nicely explains why the relaxation process hardly depends on Q in the low Q-range (Q ≤ 0.4 Å-1) and how it crosses over to a diffusion-driven process at Q ≈ Qmax. Our simulations also give support to the main assumptions of the model used to fit the experimental data in the above mentioned paper. The application of such a model to the simulation S(Q, t) data delivers (i) results for the relaxation component of S(Q, t) in agreement with those obtained from neutron experiments and (ii) longitudinal and transverse hydrodynamic-like components with similar features than those identified in previous simulations of the longitudinal and transverse current spectra directly. On the other hand, in general, our MD-simulations results of S(Q, t) qualitatively agree with the viscoelastic transition framework habitually used to describe inelastic x-ray scattering results.
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Affiliation(s)
- Fernando Alvarez
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
| | - Arantxa Arbe
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
| | - Juan Colmenero
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center MPC, Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
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6
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De Francesco A, Scaccia L, Formisano F, Guarini E, Bafile U, Maccarini M, Zhang Y, Nykypanchuck D, Alatas A, Cunsolo A. The damping of terahertz acoustic modes in aqueous nanoparticle suspensions. Sci Rep 2021; 11:20110. [PMID: 34635734 PMCID: PMC8505432 DOI: 10.1038/s41598-021-99503-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 09/20/2021] [Indexed: 11/23/2022] Open
Abstract
In this work, we investigate the possibility of controlling the acoustic damping in a liquid when nanoparticles are suspended in it. To shed light on this topic, we performed Inelastic X-Ray Scattering (IXS) measurements of the terahertz collective dynamics of aqueous suspensions of nanospheres of various materials, size, and relative concentration, either charged or neutral. A Bayesian analysis of measured spectra indicates that the damping of the two acoustic modes of water increases upon nanoparticle immersion. This effect seems particularly pronounced for the longitudinal acoustic mode, which, whenever visible at all, rapidly damps off when increasing the exchanged wavevector. Results also indicate that the observed effect strongly depends on the material the immersed nanoparticles are made of.
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Affiliation(s)
- Alessio De Francesco
- CNR-IOM & INSIDE@ILL c/o Operative Group in Grenoble (OGG), 38042, Grenoble, France
- Institut Laue-Langevin (ILL), 38042, Grenoble, France
| | - Luisa Scaccia
- Dipartimento di Economia e Diritto, Università di Macerata, Via Crescimbeni 20, 62100, Macerata, Italy
| | - Ferdinando Formisano
- CNR-IOM & INSIDE@ILL c/o Operative Group in Grenoble (OGG), 38042, Grenoble, France
- Institut Laue-Langevin (ILL), 38042, Grenoble, France
| | - Eleonora Guarini
- Dipartimento di Fisica e Astronomia, Università di Firenze, via G. Sansone 1, 50019, Sesto Fiorentino, Italy
| | - Ubaldo Bafile
- Consiglio Nazionale delle Ricerche, Istituto di Fisica Applicata "Nello Carrara", via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Marco Maccarini
- Laboratoire TIMC/IMAG UMR CNRS 5525, Université Grenoble-Alpes, 38000, Grenoble, France
| | - Yugang Zhang
- Brookhaven National Laboratory, Center for Functional Nanomaterials, P.O. Box 5000, Upton, 11973, NY, USA
| | - Dmytro Nykypanchuck
- Brookhaven National Laboratory, Center for Functional Nanomaterials, P.O. Box 5000, Upton, 11973, NY, USA
| | - Ahmet Alatas
- Argonne National Laboratory, Advanced Photon Source, P.O. Box 5000, Upton, 11973, NY, USA
| | - Alessandro Cunsolo
- Department of Physics, University of Wisconsin at Madison, 1150 University Avenue, Madison, WI, USA.
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7
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Shen Z, Ma J, Carrillo JMY, Chen WR, Sumpter BG, Wang Y. Spatiotemporal mapping of mesoscopic liquid dynamics. Phys Rev E 2021; 103:022609. [PMID: 33736070 DOI: 10.1103/physreve.103.022609] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/29/2021] [Indexed: 11/07/2022]
Abstract
The study of liquid dynamics at mesoscopic scales is still strewn with difficulty due to limitations in theory and experiment. Historically, significant attention has been given to the analysis of space-time correlation functions and their frequency-Fourier transforms at a few discrete wave numbers. The massive computing power afforded by modern high performance computing clusters and the advent of a wide-angle neutron spin-echo spectrometer, however, have unlocked a more intuitive and fruitful approach to this problem. Using molecular dynamics simulations, here we demonstrate the benefits of spatiotemporally mapping intermediate scattering functions on a dense grid of correlation times and wave numbers. Four model systems are investigated: a Lennard-Jones liquid, a coarse-grained bead-spring polymer, a molten sodium chloride, and a poly(ethylene oxide) melt. We show that the spatiotemporal mapping approach is particularly useful for elucidating the mesoscopic dynamics in these liquids, where several underlying mechanisms, such as molecular relaxations, hydrodynamic modes, and nonhydrodynamic excitations, are potentially at play. Compared to the traditional method, direct visualization of density space-time correlation functions on two-dimensional color maps permits appraisals of complicated dynamical behavior at mesoscales in a global manner. For example, the scaling relations between space and time for different types of molecular motions can be straightforwardly identified on these plots, without any model-dependent analysis. Additionally, we show how theoretical ideas regarding collective mesoscopic dynamics, such as the classical hydrodynamic theory, the convolution approximation, and a recently proposed phenomenological model, can be discussed in terms of the global features of spatiotemporal maps of intermediate scattering functions. The new perspective offered by the spatiotemporal mapping method should prove useful for the study of liquid dynamics in general.
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Affiliation(s)
- Zhiqiang Shen
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Jihong Ma
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Jan-Michael Y Carrillo
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Wei-Ren Chen
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Bobby G Sumpter
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Yangyang Wang
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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8
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Jindal A, Vasudevan S. Molecular Conformation and Hydrogen Bond Formation in Liquid Ethylene Glycol. J Phys Chem B 2020; 124:9136-9143. [PMID: 32945675 DOI: 10.1021/acs.jpcb.0c06324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ethylene glycol (EG) molecule, HOCH2CH2OH, adopts a conformation where the central OCCO dihedral is exclusively gauche in the gaseous and crystalline states, but in the liquid state, for close to 20% of the molecules, the central OCCO adopts the energetically unfavorable trans conformation. Here we report calculations, based on ab initio molecular dynamics simulations, on the thermodynamics associated with hydrogen bond formation in the liquid state of EG between donor-acceptor pairs with different molecular conformations. We establish an operational, geometric definition of hydrogen bonds in liquid EG from an analysis of the proton NMR data and show that the key feature, irrespective of the conformation, is marked directionality with almost linear ∠HO···O angles. The free energy for hydrogen bond formation estimated as the potential of mean force for the reversible work associated with the passage from a hypothetical state where hydrogen bonding is absent and donor-acceptor pairs are randomly oriented to the hydrogen-bonded state where the pairs are oriented showed comparable magnitudes irrespective of the molecular conformation of either the donor or acceptor. The results suggest that the presence of the trans conformer in liquid EG would require an understanding of its role in the extended hydrogen-bonded network of the liquid.
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Affiliation(s)
- Aman Jindal
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sukumaran Vasudevan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India
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9
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Jindal A, Vasudevan S. Geometry of OH⋯O interactions in the liquid state of linear alcohols from ab initio molecular dynamics simulations. Phys Chem Chem Phys 2020; 22:6690-6697. [DOI: 10.1039/d0cp00435a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hydrogen bonding OH···O geometries in the liquid state of linear alcohols, derived from ab initio MD simulations, show no change from methanol to pentanol, in contrast to that observed in their crystalline state.
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Affiliation(s)
- Aman Jindal
- Department of Inorganic and Physical Chemistry
- IISc
- Bangalore
- India
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10
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De Francesco A, Scaccia L, Maccarini M, Formisano F, Guarini E, Bafile U, Cunsolo A. Interpreting the Terahertz Spectrum of Complex Materials: The Unique Contribution of the Bayesian Analysis. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E2914. [PMID: 31505798 PMCID: PMC6766264 DOI: 10.3390/ma12182914] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/19/2019] [Accepted: 08/29/2019] [Indexed: 11/16/2022]
Abstract
In the last few decades, experimental studies of the terahertz spectrum of density fluctuations have considerably improved our knowledge of the mesoscopic dynamics of disordered materials, which also have imposed new demands on the data modelling and interpretation. Indeed, lineshape analyses are no longer limited to the phenomenological observation of inelastic features, as in the pioneering stage of Neutron or X-ray spectroscopy, rather aiming at the extraction from their shape of physically relevant quantities, as sound velocity and damping, relaxation times, or other transport coefficients. In this effort, researchers need to face both inherent and practical obstacles, respectively stemming from the highly damped nature of terahertz modes and the limited energy resolution, accessible kinematic region and statistical accuracy of the typical experimental outcome. To properly address these challenges, a global reconsideration of the lineshape modelling and the enforcement of evidence-based probabilistic inference is becoming crucial. Particularly compelling is the possibility of implementing Bayesian inference methods, which we illustrated here through an in-depth discussion of some results recently obtained in the analysis of Neutron and X-ray scattering results.
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Affiliation(s)
- Alessio De Francesco
- Consiglio Nazionale delle Ricerche, Istituto Officina dei Materiali, Operative Group in Grenoble (OGG), c/o Institut Laue Langevin, 38042 Grenoble, France
| | - Luisa Scaccia
- Dipartimento di Economia e Diritto, Università di Macerata, Via Crescimbeni 20, 62100 Macerata, Italy
| | - Marco Maccarini
- Laboratoire TIMC/IMAG UMR CNRS 5525 Grenoble, Université Grenoble-Alpes, 38000 Grenoble, France
| | - Ferdinando Formisano
- Consiglio Nazionale delle Ricerche, Istituto Officina dei Materiali, Operative Group in Grenoble (OGG), c/o Institut Laue Langevin, 38042 Grenoble, France
| | - Eleonora Guarini
- Dipartimento di Fisica e Astronomia, Università di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino, Italy
| | - Ubaldo Bafile
- Consiglio Nazionale delle Ricerche, Istituto di Fisica Applicata "Nello Carrara", via Madonna del Piano 10, I-50019 Sesto Fiorentino, Italy
| | - Alessandro Cunsolo
- Brookhaven National Laboratory-National Synchrotron Light Source-NSLS II, P.O. Box 5000, Upton, NY 11973, USA.
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11
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Almásy L, Kuklin AI, Požar M, Baptista A, Perera A. Microscopic origin of the scattering pre-peak in aqueous propylamine mixtures: X-ray and neutron experiments versus simulations. Phys Chem Chem Phys 2019; 21:9317-9325. [DOI: 10.1039/c9cp01137d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure of aqueous propylamine mixtures is investigated through X-ray and neutron scattering experiments, and the scattered intensities compared with computer simulation data.
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Affiliation(s)
- László Almásy
- State Key Laboratory of Environment-friendly Energy Materials
- Southwest University of Science and Technology
- Mianyang 621010
- China
- Wigner Research Centre for Physics
| | - Alexander I. Kuklin
- Frank Laboratory of Neutron Physics
- Joint Institute for Nuclear Research
- Dubna
- Russia
| | | | - Anthony Baptista
- Sorbonne Université
- Laboratoire de Physique Théorique de la Matière Condensée (UMR CNRS 7600)
- Paris cedex 05
- France
| | - Aurélien Perera
- Sorbonne Université
- Laboratoire de Physique Théorique de la Matière Condensée (UMR CNRS 7600)
- Paris cedex 05
- France
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12
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Yong CW, Todorov IT. DL_ANALYSER Notation for Atomic Interactions (DANAI): A Natural Annotation System for Molecular Interactions, Using Ethanoic Acid Liquid as a Test Case. Molecules 2017; 23:molecules23010036. [PMID: 29295538 PMCID: PMC5943928 DOI: 10.3390/molecules23010036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/20/2017] [Accepted: 12/21/2017] [Indexed: 11/16/2022] Open
Abstract
The DL_ANALYSER Notation for Atomic Interactions, DANAI, is the notation syntax to describe interactions between molecules. This notation can annotate precisely the detailed atomistic interactions without having to resolve to diagrammatic illustrations, and yet can be interpreted easily by both human users and computational means. By making use of the DL_F Notation, a universal atom typing scheme for molecular simulations, DANAI contains the expression of atomic species in a natural chemical sense. It is implemented within DL_ANALYSER, a general analysis software program for DL_POLY molecular dynamics simulation software. By making references to the molecular dynamics simulations of pure ethanoic acid liquid, it is shown that DL_ANALYSER can identify and distinguish a variety of hydrogen bond and hydrophobic contact networks through the use of the DANAI expression. It was found that the carboxylic groups preferentially orientated in a "head-to-tail" conformation to form hydrogen bonds between the carbonyl oxygen and hydroxyl hydrogen, resulting in a series of linear structures that intertwined with pockets of methyl clusters.
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Affiliation(s)
- Chin W Yong
- Scientific Computing Department, Science and Technology Facilities Council, Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, UK.
- Manchester Pharmacy School, Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9NT, UK.
| | - Ilian T Todorov
- Scientific Computing Department, Science and Technology Facilities Council, Daresbury Laboratory, Sci-Tech Daresbury, Warrington WA4 4AD, UK.
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13
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Bellissima S, González MA, Bafile U, Cunsolo A, Formisano F, De Panfilis S, Guarini E. Switching off hydrogen-bond-driven excitation modes in liquid methanol. Sci Rep 2017; 7:10057. [PMID: 28855594 PMCID: PMC5577163 DOI: 10.1038/s41598-017-10259-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/07/2017] [Indexed: 11/23/2022] Open
Abstract
Hydrogen bonding plays an essential role on intermolecular forces, and consequently on the thermodynamics of materials defined by this elusive bonding character. It determines the property of a vital liquid as water as well as many processes crucial for life. The longstanding controversy on the nature of the hydrogen bond (HB) can be settled by looking at the effect of a vanishing HB interaction on the microscopic properties of a given hydrogen-bonded fluid. This task suits the capabilities of computer simulations techniques, which allow to easily switch off HB interactions. We then use molecular dynamics to study the microscopic properties of methanol, a prototypical HB liquid. Fundamental aspects of the dynamics of methanol at room temperature were contextualised only very recently and its rich dynamics was found to have striking analogies with that of water. The lower temperature (200 K) considered in the present study led us to observe that the molecular centre-of-mass dynamics is dominated by four modes. Most importantly, the computational ability to switch on and off hydrogen bonds permitted us to identify which, among these modes, have a pure HB-origin. This clarifies the role of hydrogen bonds in liquid dynamics, disclosing new research opportunities and unexplored interpretation schemes.
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Affiliation(s)
- Stefano Bellissima
- Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, I-50019, Sesto Fiorentino, Italy
| | | | - Ubaldo Bafile
- Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, I-50019, Sesto Fiorentino, Italy
| | - Alessandro Cunsolo
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Ferdinando Formisano
- Consiglio Nazionale delle Ricerche, Istituto Officina dei materiali, Operative Group in Grenoble, F-38042, Grenoble, France
| | - Simone De Panfilis
- Istituto Italiano di Tecnologia, Center for Life Nano Science, I-00161, Roma, Italy.
| | - Eleonora Guarini
- Dipartimento di Fisica e Astronomia, Università di Firenze, I-50019, Sesto Fiorentino, Italy.
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Bertrand CE, Self JL, Copley JRD, Faraone A. Nanoscopic length scale dependence of hydrogen bonded molecular associates' dynamics in methanol. J Chem Phys 2017; 146:194501. [PMID: 28527447 PMCID: PMC5648548 DOI: 10.1063/1.4983179] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/25/2017] [Indexed: 11/14/2022] Open
Abstract
In a recent paper [C. E. Bertrand et al., J. Chem. Phys. 145, 014502 (2016)], we have shown that the collective dynamics of methanol shows a fast relaxation process related to the standard density-fluctuation heat mode and a slow non-Fickian mode originating from the hydrogen bonded molecular associates. Here we report on the length scale dependence of this slow relaxation process. Using quasielastic neutron scattering and molecular dynamics simulations, we show that the dynamics of the slow process is affected by the structuring of the associates, which is accessible through polarized neutron diffraction experiments. Using a series of partially deuterated samples, the dynamics of the associates is investigated and is found to have a similar time scale to the lifetime of hydrogen bonding in the system. Both the structural relaxation and the dynamics of the associates are thermally activated by the breaking of hydrogen bonding.
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Affiliation(s)
- C E Bertrand
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - J L Self
- McKetta Department of Chemical Engineering, University of Texas, Austin, Texas 78712, USA
| | - J R D Copley
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - A Faraone
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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15
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Zanatta M, Barocchi F, De Francesco A, Farhi E, Formisano F, Guarini E, Laloni A, Orecchini A, Paciaroni A, Petrillo C, Pilgrim WC, Suck JB, Sacchetti F. A high-flux upgrade for the BRISP spectrometer at ILL. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2017; 88:053905. [PMID: 28571465 DOI: 10.1063/1.4983572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To date, the BRISP spectrometer represents the state-of-the-art for every instrument aiming to perform Brillouin neutron scattering. Exploiting accurate ray-tracing McStas simulations, we investigate an improved configuration of the BRISP primary spectrometer to provide a higher flux at the sample position, while preserving all the present capabilities of the instrument. This configuration is based on a neutron guide system and is designed to fit the instrument platform with no modifications of the secondary spectrometer. These evaluations show that this setup can achieve a flux gain factor ranging from 3 to 6, depending on the wavelength. This can expand the experimental possibilities of BRISP towards smaller samples, possibly using also complex sample environments.
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Affiliation(s)
- M Zanatta
- Dipartimento di Informatica, Università di Verona, I-37134 Verona, Italy
| | - F Barocchi
- Dipartimento di Fisica e Astronomia, Università di Firenze, I-50019 Sesto Fiorentino, Italy
| | - A De Francesco
- IOM-CNR, Operative Group in Grenoble (OGG), c/o Institut Laue Langevin, F-38042 Grenoble, France
| | - E Farhi
- Institut Laue Langevin, F-38042 Grenoble, France
| | - F Formisano
- IOM-CNR, Operative Group in Grenoble (OGG), c/o Institut Laue Langevin, F-38042 Grenoble, France
| | - E Guarini
- Dipartimento di Fisica e Astronomia, Università di Firenze, I-50019 Sesto Fiorentino, Italy
| | - A Laloni
- IOM-CNR, Operative Group in Grenoble (OGG), c/o Institut Laue Langevin, F-38042 Grenoble, France
| | - A Orecchini
- Dipartimento di Fisica e Geologia, Università di Perugia, I-06123 Perugia, Italy
| | - A Paciaroni
- IOM-CNR, c/o Dipartimento di Fisica e Geologia, Università di Perugia, I-06123 Perugia, Italy
| | - C Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, I-06123 Perugia, Italy
| | - W-C Pilgrim
- Physikalische Chemie, Philipps Universität Marburg, D-35032 Marburg, Germany
| | - J-B Suck
- Institute of Physics, Technische Universität Chemnitz, D-09107 Chemnitz, Germany
| | - F Sacchetti
- Dipartimento di Fisica e Geologia, Università di Perugia, I-06123 Perugia, Italy
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16
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Ljungberg MP, Zhovtobriukh I, Takahashi O, Pettersson LGM. Core-hole-induced dynamical effects in the x-ray emission spectrum of liquid methanol. J Chem Phys 2017; 146:134506. [PMID: 28390372 DOI: 10.1063/1.4979656] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We compute the x-ray emission spectrum of liquid methanol, with the dynamical effects that result from the creation of the core hole included in a semiclassical way. Our method closely reproduces a fully quantum mechanical description of the dynamical effects for relevant one-dimensional models of the hydrogen-bonded methanol molecules. For the liquid, we find excellent agreement with the experimental spectrum, including the large isotope effect in the first split peak. The dynamical effects depend sensitively on the initial structure in terms of the local hydrogen-bonding (H-bonding) character: non-donor molecules contribute mainly to the high-energy peak while molecules with a strong donating H-bond contribute to the peak at lower energy. The spectrum thus reflects the initial structure mediated by the dynamical effects that are, however, seen to be crucial in order to reproduce the intensity distribution of the recently measured spectrum.
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Affiliation(s)
- M P Ljungberg
- Donostia International Physics Center, Paseo Manuel de Lardizabal, 4, E-20018 Donostia-San Sebastián, Spain
| | - I Zhovtobriukh
- FYSIKUM, Stockholm University, AlbaNova, S-106 91 Stockholm, Sweden
| | - O Takahashi
- Institute for Sustainable Sciences and Development, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - L G M Pettersson
- FYSIKUM, Stockholm University, AlbaNova, S-106 91 Stockholm, Sweden
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17
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Guarini E, Bellissima S, Bafile U, Farhi E, De Francesco A, Formisano F, Barocchi F. Density of states from mode expansion of the self-dynamic structure factor of a liquid metal. Phys Rev E 2017; 95:012141. [PMID: 28208346 DOI: 10.1103/physreve.95.012141] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Indexed: 11/07/2022]
Abstract
We show that by exploiting multi-Lorentzian fits of the self-dynamic structure factor at various wave vectors it is possible to carefully perform the Q→0 extrapolation required to determine the spectrum Z(ω) of the velocity autocorrelation function of a liquid. The smooth Q dependence of the fit parameters makes their extrapolation to Q=0 a simple procedure from which Z(ω) becomes computable, with the great advantage of solving the problems related to resolution broadening of either experimental or simulated self-spectra. Determination of a single-particle property like the spectrum of the velocity autocorrelation function turns out to be crucial to understanding the whole dynamics of the liquid. In fact, we demonstrate a clear link between the collective mode frequencies and the shape of the frequency distribution Z(ω). In the specific case considered in this work, i.e., liquid Au, analysis of Z(ω) revealed the presence, along with propagating sound waves, of lower frequency modes that were not observed before by means of dynamic structure factor measurements. By exploiting ab initio simulations for this liquid metal we could also calculate the transverse current-current correlation spectra and clearly identify the transverse nature of the above mentioned less energetic modes. Evidence of propagating transverse excitations has actually been reported in various works in the recent literature. However, in some cases, like the present one, these modes are difficult to detect in density fluctuation spectra. We show here that the analysis of the single-particle dynamics is able to unveil their presence in a very effective way. The properties here shown to characterize Z(ω), and the information in it contained therefore allow us to identify it with the density of states (DoS) of the liquid. We demonstrate that only nonhydrodynamic modes contribute to the DoS, thus establishing its purely microscopic origin. Finally, as a by-product of this work, we provide our estimate of the self-diffusion coefficient of liquid gold just above melting.
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Affiliation(s)
- E Guarini
- Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino, Italy
| | - S Bellissima
- Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino, Italy.,Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, via Madonna del Piano 10, I-50019 Sesto Fiorentino, Italy
| | - U Bafile
- Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, via Madonna del Piano 10, I-50019 Sesto Fiorentino, Italy
| | - E Farhi
- Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, F-38042 Grenoble Cedex 9, France
| | - A De Francesco
- Consiglio Nazionale delle Ricerche, Istituto Officina dei Materiali c/o Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, F-38042 Grenoble Cedex 9, France
| | - F Formisano
- Consiglio Nazionale delle Ricerche, Istituto Officina dei Materiali c/o Institut Laue-Langevin, 71 avenue des Martyrs, CS 20156, F-38042 Grenoble Cedex 9, France
| | - F Barocchi
- Dipartimento di Fisica e Astronomia, Università degli Studi di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino, Italy
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