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AbINS: The modern software for INS interpretation

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Abstract

Inelastic neutron scattering (INS) spectroscopy, contrary to other vibrational spectroscopic techniques such as infrared or Raman spectroscopies, provides much richer microscopic insight into a material due to the absence of selection rules induced by the system's symmetry and via its dependence on both energy (E) and momentum (Q) transfer. First-principles density functional theory (DFT) based calculations are now routinely used to interpret infrared and Raman spectra. These calculations can also be used to interpret INS spectra, however, the need to include the neutron scattering cross sections, overtones and combination modes, together with instrument specific E-Q windows make the data analysis challenging. Here we present AbINS: a new generation of software to interpret INS spectra using ab initio phonon data. AbINS is an open-source package implemented as a plugin to the neutron data analysis software, Mantid and offers the facility to plot the full (Q, E) map for powder samples, with the option to extract individual atomic contributions. This option is then applied to analyse the vibrational spectrum of non-hydrogenous K2SiF6 to extract atom-type contributions identifying T1g librational mode of the [SiF6]2- ion together with the T2u F-Si-F bending mode.

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... Normal mode frequencies and eigenvectors are determined by lattice dynamics calculations at the Γ-point of the resulting ground state structure by diagonalisation of dynamical matrices using the density-functional perturbation theory (DFPT) and linear-response methods [20]. INS spectra are obtained from calculated eigenenergies and eigenvectors and using the abINS algorithm in Mantid [21]. ...
... where, e i,m is the eigenvector of atom i in mode m, Q is the momentum-transfer vector, M i is the mass of atom i and W (Q, T) is the Debye-Waller (DW) factor at temperature T. At very low temperatures, the DW term is approximated as zero. For an inverted-geometry INS spectrometer like TOSCA, Q 2 is proportional to E. A powder averaging has been applied in this calculation following standard methodology [21][22][23]. ...
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Lattice dynamics in organic ferroelectric PhMDA (2-phenylmalondialdehyde C 9 H 8 O 2 ) has been investigated using inelastic neutron scattering (INS) spectroscopy and first principles based calculations. Most of the prominent features of the INS spectrum originated from the normal modes of hydrogen bonded malondialdehyde (MDA) units rather than from phenyl rings. It is also found that carbon-hydrogen bonds in the MDA unit are tighter than these in phenyl rings. From the calculated splitting of LO (longitudinal optical) and TO (transverse optical) normal modes, it is predicted that hydrogen bonds in MDA units, which hold the solid state structure, contribute more to the ferroelectric polarisation of PhMDA. Any distortion of H-ions in these hydrogen bonds thus affects ferroelectric properties of this material.
... Nuances involving the weighting of each mode with neutron cross-sections, combinations, and overtones of the fundamental modes (and in turn, their relative weighting), along with instrumental factors, must be applied to make a quantitative comparison between theory and experiment. The newly launched software package AbINS [6] provides these capabilities and aims to give comprehensive support to as many DFT codes as possible (currently including Gaussian, CASTEP, CRYSTAL, and VASP). The package is neatly included as an algorithm within the widely used neutron scattering analysis software package 'Mantid' [7], allowing a direct comparison of neutron and in-silico data. ...
... A recent combination of INS and DFT lattice dynamics has highlighted the crucial importance of hydrogen bonding for phase evolution [10]. In this work, Kieslich and co-workers correlated the vibrational spectra collected from INS with calculated phonons, using the ABINS package [6]. Crucially the study reports that hydrogen-bonding, configurational entropy, and vibrational entropy in a model HOIP system are all of the same order of magnitude. ...
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Recent developments in first-principles lattice dynamics and classical force field based molecular dynamics are revolutionising the field of neutron spectroscopy. Herein we present a short review of these methods, their critical role in the supporting of cutting-edge experiments, and how they are improved by matching experimental data. We begin with a brief overview of how lattice dynamics calculations can be compared to inelastic neutron scattering (INS) and molecular dynamics simulations to both INS and quasi-elastic neutron scattering (QENS). We then provide a series of exemplar applications where lattice dynamics and molecular dynamics have been used in conjunction with neutron spectroscopy to bring significant understanding to topical areas of materials science namely: (i) lattice dynamics and INS for the study of hybrid organic-inorganic perovskites (ii) lattice dynamics and INS for the study of flexible porous solids and (iii) molecular dynamics and QENS for probing molecular behaviour in zeolite catalysis. In all three cases, the understanding gained through the synergy of experiment and computation would have been significantly reduced using either in isolation. Finally, we consider the current state of the art, describing outstanding challenges and suggesting future directions in this exciting and fertile area of physical science.
... After geometry optimization, the vibrational spectra were calculated in the harmonic approximation using density functional perturbation theory [17]. This procedure generates the vibrational eigenvalues and eigenvectors, which allows visualization of the modes within Materials Studio (http://accelrys.com/products/collaborative-science/bioviamaterials-studio/) and is also the information needed to calculate the INS spectrum using either the programs ACLIMAX [18] or AbINS [19]. We emphasize that the transition energies have not been scaled. ...
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In this work, we have used a combination of vibrational spectroscopy (infrared, Raman and inelastic neutron scattering) and periodic density functional theory to investigate six metal methanesulfonate compounds that exhibit four different modes of complexation of the methanesulfonate ion: ionic, monodentate, bidentate and pentadentate. We found that the transition energies of the modes associated with the methyl group (C–H stretches and deformations, methyl rock and torsion) are essentially independent of the mode of coordination. The SO3 modes in the Raman spectra also show little variation. In the infrared spectra, there is a clear distinction between ionic (i.e. not coordinated) and coordinated forms of the methanesulfonate ion. This is manifested as a splitting of the asymmetric S–O stretch modes of the SO3 moiety. Unfortunately, no further differentiation between the various modes of coordination: unidentate, bidentate etc… is possible with the compounds examined. While it is likely that such a distinction could be made, this will require a much larger dataset of compounds for which both structural and spectroscopic data are available than that available here.
... The provided phonon frequencies and eigenvectors were used directly for the INS modeling. The calculations of the dynamic structure factor, S(Q, ω), were performed with the help of the AbINS program [41]. ...
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We present a joint experimental and computational terahertz (THz) spectroscopy study of the most stable polymorph (form I) of an antihypertensive pharmaceutical solid, felodipine (FLD). The vibrational response has been analyzed at room temperature by combining optical (THz-TDS, FT-IR, THz-Raman) and neutron (INS) terahertz spectroscopy. With the challenging example of a large and flexible molecular solid, we illustrate the complementarity of the experimental techniques. We show how the results can be understood by employing ab initio modeling and discuss current progress in the field. To this end, we employ plane wave formulation of density functional theory (plane wave DFT) along with harmonic lattice dynamics calculations (HLD) and ab initio molecular dynamics (AIMD) simulations. Based on a comprehensive theoretical analysis, we discover an inconsistency in the commonly accepted structural model, which can be linked to a distinct librational dynamics of the side ester chains. As a result, only a moderate agreement with the experimental spectra can be achieved. We, therefore, propose an alternative structural model, effectively accounting for the influence of the large-amplitude librations and allowing for a comprehensive analysis of the vibrational resonances up to 4.5 THz. In that way, we illustrate the applicability of the computationally supported THz spectroscopy to detect subtle structural issues in molecular solids. While the provided structural model can be treated as a guess, the problem calls for further revision by means of high-resolution crystallography. The problem also draws a need of extending the THz experiments toward low-temperature conditions and single-crystal samples. On the other hand, the studied system emerges as a challenge for the DFT modeling, being extremely sensitive to the level of the theory used and the resulting description of the intermolecular forces. FLD form I can be, hence, considered as a testbed for the use of more sophisticated theoretical approaches, particularly relying on an advanced treatment of the van der Walls forces and going beyond zero-temperature conditions and harmonic approximation.
... The visualisations of the modes were carried out in Materials Studio 2017 (version R2(17.2.0.1626), BIOVIA) [49] and the INS spectra were generated with ACLIMAX (version 6.0.0 LE) [50] or AbINS (version 1) [51]. ...
Article
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We have investigated caesium hydrogen sulfate, CsHSO4, in all three of its ambient pressure phases by total scattering neutron diffraction, inelastic neutron scattering (INS) and Raman spectroscopies and periodic density functional theory calculations. Above 140 °C, CsHSO4, undergoes a phase transition to a superprotonic conductor that has potential application in intermediate temperature fuel cells. Total scattering neutron diffraction data clearly show that all the existing structures of this phase are unable to describe the local structure, because they have either partial occupancies of the atoms and/or non-physical O–H distances. Knowledge of the local structure is crucial because it is this that determines the conduction mechanism. Starting from one of the previous models, we have generated a new structure that has no partial occupancies and reasonable O–H distances. After geometry optimisation, the calculated radial distribution function is in reasonable agreement with the experimental data, as are the calculated and observed INS and Raman spectra. This work is particularly notable in that we have measured INS spectra in the O–H stretch region above room temperature, which is extremely rare. The INS spectra have the enormous advantage that the electrical anharmonicity that complicates the infrared spectra is absent and the stretch modes are plainly seen.
... Phonon calculation was weighted with the neutron scattering cross sections included with AbINS in the Mantid software to obtain in silico spectra for comparison with the experimental INS spectra. [44,45]. ...
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The volumetric hydrogen density of 160 kg H/m3 in TiVCrNbH8 is among the highest for interstitial hydrides, but the reported reversible capacity is only about 2/3 of the full theoretical capacity at room temperature. In the present work we have investigated the local structure in TiVCrNbDx, x=0, 2.2, 8 with the aim to unravel how the remaining sites can be destabilized with respect to hydrogen/deuterium occupation using total scattering measurements and Reverse Monte Carlo (RMC) structure modelling. Our analysis indicates that the partially desorbed deuteride (x=2.2) adopts a body-centred tetragonal structure (I4/mmm) where the deuterium atoms occupy both tetrahedral and octahedral interstices with low occupancies. There is a significantly higher portion of occupied sites with nearest-neighbour metals with low valence-electron concentration VEC. This observation is used to motivate strategies for further destabilization of the hydride. Inelastic neutron scattering (INS) and density functional theory calculations (DFT) indicate that the vibrational density of states is very diverse in TiVCrNbH2.4, and it is suggested that the hydrogen atoms might be mobile between nearby interstices.
... All data processing was done using Mantid. 83 INS spectra were simulated using ABINS, 84 as implemented in Mantid. Only first-order quantum events (i.e. the fundamentals) are considered in the simulation of INS spectra. ...
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The ease with which an energetic material (explosives, propellants, and pyrotechnics) can be initiated is a critical parameter to as-sess their safety and application. Impact sensitivity parameters are traditionally derived experimentally, at great cost and risk to safety. In this work we explore a fully ab initio approach based on concepts of vibrational energy transfer to predict impact sensi-tivities for a series of chemically, structurally and energetically diverse molecular materials. The quality of DFT calculations is as-sessed for a subset of the materials by comparison with experimental inelastic neutron scattering spectra (INS). A variety of mod-els are considered, including both qualitative and quantitative analysis of the vibrational spectra. Excellent agreement against ex-perimental impact sensitivity is achieved by consideration of a multi-phonon ladder-type up-pumping mechanism that includes both overtone and combination pathways, and is improved further by the added consideration of temperature. This fully ab initio approach not only permits ranking of energetic materials in terms of their impact sensitivity but also provides a tool to guide the targeted design of advanced energetic compounds with tailored properties.
... DFPT was also used to compute the dielectric response and the Born effective charges and, from these, the infrared absorptivity was calculated. INS spectra were generated from the Gaussian09 and CASTEP outputs using AbINS [18]. Figure 2 shows the FT-Raman, infrared and INS spectra of Fe 2 (CO) 9 . ...
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Diiron nonacarbonyl, Fe2(CO)9, was discovered in 1905 and was the third metal carbonyl to be found. It was the first to be synthesized by a photochemical route. This is a challenging material to study: it is insoluble in virtually all solvents and decomposes at 373 K before melting. This means that only solid-state spectroscopic data are available. New infrared, Raman and inelastic neutron scattering (INS) spectra have been measured and used to generate a complete assignment of the vibrational spectra of Fe2(CO)9. Density functional theory (DFT) calculations are used to support the assignments; however, for this material, they are much less useful than expected, although the calculated intensities provide crucial information.
... The spectral resolution of TOSCA is similar to that of infrared and Raman techniques, approximately 2 % of the energy in question. The sample was studied at a temperature of ~10 K using a dedicated closed-cycle helium refrigerator, so as to minimize the effect of the Debye Waller factor, thus allowing us to fully distinguish the individual peaks.60 5. Organic Field-Effect Transistors (OFETs)Materials: Octadecyltrimethoxysilane (OTMS) was purchased from Fluorochem and used as received (storage under a N2 atmosphere to prevent hydrolysis). Highly doped n-type Si (100) wafers (resistivity < 0.005 Ω cm, Active Business Company GmbH) were used as the substrates for thin film transistors fabrication. ...
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Molecular vibrations play a critical role in the charge transport properties of weakly van der Waals bonded organic semiconductors. To understand which specific phonon modes contribute most strongly to the electron - phonon coupling and ensuing thermal energetic disorder in some of the most widely studied high mobility molecular semiconductors, we have combined state-of-the-art quantum mechanical simulations of the vibrational modes and the ensuing electron phonon coupling constants with experimental measurements of the low-frequency vibrations using inelastic neutron scattering and terahertz time-domain spectroscopy. In this way we have been able to identify the long-axis sliding motion as a killer phonon mode, which in some molecules contributes more than 80% to the total thermal disorder. Based on this insight, we propose a way to rationalize mobility trends between different materials and derive important molecular design guidelines for new high mobility molecular semiconductors.
... The DFT phonon calculations can be precisely weighted to the neutronic response of the spectrometer. 17,18 Neutronic weighting of the DFT phonon spectra and subsequent comparison with INS showed a strong agreement for both the protiated and deuteriated cases (see Figure 2a and Figure 2b). It was validated that the major differences in the H 15 and D 15 spectra come from the deuteriation contrast of the Cp*, whereby motions in the deuteriated Cp* become invisible by The Journal of Physical Chemistry Letters pubs.acs.org/JPCL ...
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[(Pentamethylcyclopentadienyl)Rh(III)(bipyridine)(chloride)]+ (Cp*Rh-Cl) undergoes sequential deuteriation of its 15 Cp* CH groups in polar deuterated solvents. Vibrational spectra of H 14 -Cp*Rh-Cl and D 14 -Cp*Rh-Cl were captured via inelastic neutron spectroscopy (INS) and assigned using density functional theory (DFT) phonon calculations. These calculations were precisely weighted to the spectrometer's neutronic response. The Cp* ring behaves as a moving carousel, bringing each CH3 close to the Rh-OH/D center where proton abstraction occurs. Vibrations relevant for carousel movement and proximal positioning for H transfer were identified. DFT modeling uncovered changes in vibrations along the reaction path, involving a Rh(I)-fulvene intermediate. Vibronic energy contributions are large across the entire transition. Remarkably, they amount to over a 400-fold increase in the proton transfer rate. The inclusion of vibrational degrees of freedom could be applied more widely to catalysts and molecular machines to harness the energetics of these vibrations and increase their effective rates of operation.
... The INS spectra were modeled in both HLD and AIMD schemes. . [32][33][34]36 Additional experimental and computational details are provided in the Supporting Information. figure (a) shows the total (thick gray curve) and partial (thin gray curves) hydrogen-projected VDOSs for each of the 48 FA + of the model presented in Figure S3b. ...
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The vibrational dynamics of pure and methylammonium-doped formamidinium lead iodide perovskites (FAPbI3) has been investigated by high-resolution neutron spectroscopy. For the first time, we provide an exhaustive and accurate analysis of the cation vibrations and underlying local structure around the organic moiety in these materials using first-principles electronic-structure calculations validated by the neutron data. Inelastic neutron scattering experiments on FAPbI3 provide direct evidence of the formation of a low-temperature orientational glass, unveiling the physicochemical origin of phase metastability in the tetragonal structure. Further analysis of these data provides a suitable starting point to explore and understand the stabilization of the perovskite framework via doping with small amounts of organic cations. In particular, we find that the hydrogen-bonding interactions around the formamidinium cations are strengthened as a result of cage deformation. This synergistic effect across perovskite cages is accompanied by a concomitant weakening of the methylammonium interactions with the surrounding framework.
... This Non-diagonal Supercell Method (NCM) takes advantage of the periodicity of the system allowing a calculation of the dynamical matrix using supercells, which are much smaller than those used in DM calculations and, hence, more efficient. To date, a number of codes have also been developed to simulate neutron observables directly from HLD outputs [162,171,[175][176][177][178][179][180]. ...
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This work provides an up-to-date overview of recent developments in neutron spectroscopic techniques and associated computational tools to interrogate the structural properties and dynamical behavior of complex and disordered materials, with a focus on those of a soft and polymeric nature. These have and continue to pave the way for new scientific opportunities simply thought unthinkable not so long ago, and have particularly benefited from advances in high-resolution, broadband techniques spanning energy transfers from the meV to the eV. Topical areas include the identification and robust assignment of low-energy modes underpinning functionality in soft solids and supramolecular frameworks, or the quantification in the laboratory of hitherto unexplored nuclear quantum effects dictating thermodynamic properties. In addition to novel classes of materials, we also discuss recent discoveries around water and its phase diagram, which continue to surprise us. All throughout, emphasis is placed on linking these ongoing and exciting experimental and computational developments to specific scientific questions in the context of the discovery of new materials for sustainable technologies.
... Equation (1) allows one to predict INS features if the eigenvectors and eigenvalues are known, for example, from DFT calculations. The AbINS [39] plugin for MANTID [40] program was used for this purpose. ...
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The new complex of N,N-Dimethylglycine (DMG) with chloranilic acid (CLA) was synthesized and examined for thermal, structural, and dynamical properties. The structure of the reaction product between DMG and CLA was investigated in a deuterated dimethyl sulfoxide (DMSO-d6) solution and in the solid state by Nuclear Magnetic Resonance (NMR) (Cross Polarization Magic Angle Spinning-CPMAS NMR). The formation of the 1:1 complex of CLA and DMG in the DMSO solution was also confirmed by diffusion measurement. X-ray single crystal diffraction results revealed that the N,N-dimethylglycine–chloranilic acid (DMG+–CLA−) complex crystallizes in the centrosymmetric triclinic P-1 space group. The X-ray diffraction and NMR spectroscopy show the presence of the protonated form of N,N-dimethylglycine and the deprotonated form of chloranilic acid molecules. The vibrational properties of the co-crystal were investigated by the use of neutron (INS), infrared (IR), and Raman (RS) spectroscopies, as well as the density functional theory (DFT) with periodic boundary conditions. From the band shape analysis of the N–CH3 bending vibration, we can conclude that the CH3 groups perform fast (τR » 10−11 to 10‒13 s) reorientational motions down to a temperature of 140 K, with activation energy at ca. 6.7 kJmol–1. X-ray diffraction and IR investigations confirm the presence of a strong N+–H···O− hydrogen bond in the studied co-crystal.
... The eigenvectors (atomic displacements) for each normal mode that are part of the CASTEP and G09 output were used to visualize the modes with program Jmol [24] and to generate the INS spectrum using the program AbINS [25]. AbINS is an open-source package implemented as a plugin to the neutron data analysis software Mantid [17]. ...
Article
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The dynamics of 2-methoxybenzaldehyde, 4-methoxybenzaldehyde, and 4-ethoxybenzaldehyde in the solid state are assessed through INS spectroscopy combined with periodic DFT calculations. In the absence of experimental data for 4-ethoxybenzaldehyde, a tentative crystal structure, based on its similarity with 4-methoxybenzaldehyde, is considered and evaluated. The excellent agreement between calculated and experimental spectra allows a confident assignment of the vibrational modes. Several spectral features in the INS spectra are unambiguously assigned and torsional potential barriers for the methyl groups are derived from experimental frequencies. The intramolecular nature of the potential energy barrier for methyl rotation about O–CH3 bonds compares with the one reported for torsion about saturated C–CH3 bonds. On the other hand, the intermolecular contribution to the potential energy barrier may represent 1/3 of the barrier height in these systems.
... The phonon eigenvalues and eigenvectors were used for direct simulation of the TOSCA spectrum. 72,73 The atom-projected vibrational densities of states (apVDOSs), obtained from the LD simulations, were also used for calculating the NMD widths of the atomic species (σ j ), according to the methodology extensively described elsewhere. 30,31,60 A series of classical AIMD simulations following the Born− Oppenheimer approximation (BOMD) were performed at T = 10, 100, 200, and 300 K for a number of structural configurations considered. ...
... The resulting phonon eigenvalues and eigenvectors were used for the simulation of the TOSCA spectra. 38,39 Isotopic substitution was accounted for via the use of the appropriate neutron-scattering cross section for each isotope. ...
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Diethylammonium nitrate, [N0 0 2 2][NO3], and its perdeuterated analogue, [ND D 2 2] [NO3], were structurally characterized and studied by infrared, Raman, and inelastic neutron scattering (INS) spectroscopy. Using these experimental data along with state-of-the-art computational materials modeling, we report unambiguous spectroscopic signatures of hydrogen-bonding interactions between the two counterions. An exhaustive assignment of the spectral features observed with each technique has been provided, and a number of distinct modes related to NH···O dynamics have been identified. We put a particular emphasis on a detailed interpretation of the high-resolution, broadband INS experiments. In particular, the INS data highlight the importance of conformational degrees of freedom within the alkyl chains, a ubiquitous feature of ionic liquid (IL) systems. These findings also enable an in-depth physicochemical understanding of protonic IL systems, a first and necessary step to the tailoring of hydrogen-bonding networks in this important class of materials.
... This Non-diagonal Supercell Method (NCM) takes advantage of the periodicity of the system allowing a calculation of the dynamical matrix using supercells, which are much smaller than those used in DM calculations and, hence, more efficient. To date, a number of codes have also been developed to simulate neutron observables directly from HLD outputs [162,171,[175][176][177][178][179][180]. ...
Preprint
div>The vibrational dynamics of pure and methylammonium-doped formamidinium lead iodide perovskites (FAPbI3) has been investigated by high-resolution neutron spectroscopy. For the ?first time, we provide an exhaustive and accurate analysis of the cation vibrations and underlying local structure around the organic moiety in these materials using ?first-principles electronic-structure calculations validated by the neutron data. Inelastic Neutron Scattering experiments on FAPbI3 provide direct evidence of the formation of a low-temperature orientational glass, unveiling the physico-chemical origin of phase metastability in the tetragonal structure. Further analysis of these data provides a suitable starting point to understand and explore the stabilization of the perovskite framework via doping with small amounts of organic cations. In particular, we ?find that hydrogen bonds in FAPbI3 are strengthened in a synergistic manner as a result of cage deformation induced by the dynamics of the neighbouring methylammonium cations.</div
... The atomic displacements for each normal mode (obtained from the CASTEP and G09 outputs) were used by the program Jmol [21] to visualize the modes, as well as to generate the INS spectrum through the program AbINS [22]. AbINS, an open-source package implemented as a plugin to the neutron data-analysis software Mantid [13] accounts for the neutron-scattering cross sections, overtones and combination modes. ...
Article
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The structure and dynamics of crystalline 4-(dimethylamino) benzaldehyde, 4DMAB, are assessed through INS spectroscopy combined with periodic DFT calculations. The excellent agreement between experimental and calculated spectra is the basis for a reliable assignment of INS bands. The external phonon modes of crystalline 4DMAB are quite well described by the simulated spectrum, as well as the modes involving low-frequency molecular vibrations. Crystal field splitting is predicted and observed for the modes assigned to the dimethylamino group. Concerning the torsional motion of methyl groups, four individual bands are identified and assigned to specific methyl groups in the asymmetric unit. The torsional frequencies of the four methyl groups in the asymmetric unit fall in a region of ca. 190 ± 20 cm−1, close to the range of values observed for methyl groups bonding to unsaturated carbon atoms. The hybridization state of the X atom in X-CH3 seems to play a key role in determining the methyl torsional frequency.
... Its chief benefits are its highly penetrating nature, the absence of hard spectroscopic selection rules, and a very high incoherent neutron-scattering cross-section for the proton, providing extreme sensitivity to motions involving hydrogen atoms. In addition, the past decade has witnessed a very rapid increase in the quantity and quality of combined in-silico and INS studies, giving unprecedented clarity to a range of chemical phenomena at the atomic scale [4,5,6]. Some examples include the understanding of phase transitions [7,8,9], quantifying the role of vibrations to the kinetics in catalytic processes [10] and gas absorption in porous media [11]. ...
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Following significant instrument upgrades and parallel methodological developments over the past decade, the TOSCA neutron spectrometer at the ISIS Pulsed Neutron & Muon Source in the United Kingdom has developed a rich and growing scientific community spanning a broad range of non-traditional areas of neutron science, including chemical catalysis, gas adsorption & storage, and new materials for energy and sustainability. High-pressure science, however, has seen little to no representation to date owing to previous limitations in capability. Herein, we explore for the first time the viability of rapid high-pressure measurements in the gigapascal regime, capitalizing from the orders-of-magnitude increase in incident flux afforded by a recent upgrade of the primary-beam path. In particular, we show that spectroscopic measurements up to pressures of 2 GPa over an unprecedented energy-transfer range are now possible within the hour timescale. In addition, we have designed and commissioned a dedicated set of high-pressure vessels, with a view to foster and support the further growth and development of an entirely new user community on TOSCA.
... [19] INS spectra are obtained from calculated eigenvectors and eigenenergies using the newly implemented abINS algorithm in Mantid. [20,21] In the calculations of INS spectra, fundamentals, overtones and combination bands are included up to fourth order. Born effective charge tensors and LO-TO splitting of normal modes are calculated as implemented in the CASTEP code [15]. ...
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Structure and dynamics of hydrogen bonded organic ferroelectric CBDC (1-cyclobutene-1,2-dicarboxylic acid, C 6 H 8 O 4 ) have been investigated using inelastic neutron scattering (INS) spectroscopy and first principles lattice dynamics. Vibrational modes of O–H–O bending, related with two different types of hydrogen bonds, inter and intra-molecular, are manifested as two sets of doublets in the range of 900–1400 cm ⁻¹ in the INS spectrum. First principles density functional theory (DFT) is used to assign these doublets to out-of-the-plane and in-plane vibrations of these two types of O–H—O bending modes. Correlating structure and dynamics we find that although the local structures of the hydrogen bonded protons are similar, their medium range order may influence their vibrational frequencies. Vibrational modes of non-hydrogen bonded protons also are assigned separately in the spectrum. Comparing the calculated and the experimental INS spectra it is predicted that hydrogen bonded O–H bonds are more anharmonic than non-hydrogen bonded C–H bonds. From the calculated Born effective charge tensor it is predicted that inter-molecular hydrogen bonds contribute more to the ferroelectric polarisation of CBDC than intra-molecular ones. A large LO-TO splitting of the O–H stretching mode at 2471 cm ⁻¹ is identified with the mode that has significant contribution to the ferroelectric polarisation. As this mode is sensitive to long range Coulomb interactions and is responsible for ferroelectric properties of the material, vibrational spectroscopy combined with DFT calculations is proposed as a characterisation tool to investigate ferroelectric properties in the CBDC molecular crystal.
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Both structural glasses and disordered crystals are known to exhibit anomalous thermal, vibrational, and acoustic properties at low temperatures or low energies, what is still a matter of lively debate. To shed light on this issue, we studied the halomethane family CBrnCl4−n (n=0,1,2) at low temperature where, despite being perfectly translationally ordered stable monoclinic crystals, glassy dynamical features had been reported from experiments and molecular dynamics simulations. For n=1,2 dynamic disorder originates by the random occupancy of the same lattice sites by either Cl or Br atoms, but not for the ideal reference case of CCl4. Measurements of the low-temperature specific heat (Cp) for all these materials are here reported, which provide evidence of the presence of a broad peak in Debye-reduced Cp(T)/T3 and in the reduced density of states (g(ω)/ω2) determined by means of neutron spectroscopy, as well as a linear term in Cp usually ascribed in glasses to two-level systems in addition to the cubic term expected for a fully ordered crystal. Being CCl4 a fully ordered crystal, we also performed density functional theory (DFT) calculations, which provide unprecedented detailed information about the microscopic nature of vibrations responsible for that broad peak, much alike the “'boson peak” of glasses, finding it to essentially arise from a piling up (at around 3–4 meV) of low-energy optical modes together with acoustic modes near the Brillouin-zone limits.
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We present a complex, computationally-supported solid-state spectroscopy study, elucidating the local order in a blockbuster anti-ulcer drug, ranitidine hydrochloride form II. To this end, dispersion-corrected periodic density functional theory calculations were combined with powder X-Ray diffraction, solid-state nuclear magnetic resonance, and low-frequency vibrational spectroscopy, delivering a refined structural model. We found that a competition of nearly iso-energetic sub-structures, formed by enamine type species, give rise to the formation of several potential polymorphs. The considered models were critically examined both in terms of the stabilization energy and the spectral response. While previous studies left the crystal structure considered as a conformationally disordered at a molecular level, we found that the disorder is realized far beyond the local molecular arrangement, elucidating formation of infinite nets of hydrogen-bonded chains, linking both \textit{Z} and \textit{E} enamine fragments. On the contrary to the previously proposed model, such an arrangement is found to be highly energy favorable, disclosing the source of a high-stability of the form II. An improved atomistic model has been proposed, successfully accounting for all available spectroscopic data. Particularly, we examine the presented structural arrangement to perfectly describe both optical and neutron terahertz fingerprints, representing string and robust assessment of the validity of the crystal structure with its sensitivity to the crystal packing and the intermolecular forces present therein.
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We report a pressure-induced transition to a new crystalline phase of biurea (C2D6N4O2). Neutron-powder diffraction and Raman spectra, measured up to 3.89 GPa reveal this transition to be isosymmetric, where substantial intramolecular reorientation leads to an abrupt decrease in unit cell volume at ∼0.6 GPa and an increase in some intermolecular contact distances. DFT and vibrational energy calculations suggest that the ambient pressure phase is stabilised by zero point energy and entropy, until the pressure–volume–driven transition at 0.6 GPa.
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Molecular vibrations play a critical role in the charge transport properties of weakly van der Waals bonded organic semiconductors. To understand which specific phonon modes contribute most strongly to the electron–phonon coupling and ensuing thermal energetic disorder in some of the most widely studied high‐mobility molecular semiconductors, state‐of‐the‐art quantum mechanical simulations of the vibrational modes and the ensuing electron–phonon coupling constants are combined with experimental measurements of the low‐frequency vibrations using inelastic neutron scattering and terahertz time‐domain spectroscopy. In this way, the long‐axis sliding motion is identified as a “killer” phonon mode, which in some molecules contributes more than 80% to the total thermal disorder. Based on this insight, a way to rationalize mobility trends between different materials and derive important molecular design guidelines for new high‐mobility molecular semiconductors is suggested.
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How the methyl torsion transition energy in unsaturated systems is affected by its environment is investigated. It is strongly influenced by both its immediate neighborhood, (the number of methyl groups present in the molecule) and the intermolecular interactions. It is clear that the intermolecular interactions have a major influence on the torsion transition energy, as demonstrated unambiguously previously for mesitylene and also seen here for other systems. In part, this may be caused by the fact that the methyl torsion is rarely a pure mode (unless enforced by symmetry). Where the crystal structure is available, the assignments have been supported by CASTEP calculations of the unit cell. The agreement between the observed and calculated spectra is generally good, although not perfect, toluene being a case in point, and highlights just how demanding it is to obtain accurate transition energies for low energy modes. The disagreement between observed and calculated inelastic neutron scattering spectra for meta-xylene and 9,10 dimethylanthracene is so severe that it would suggest that there are additional phases to those presently known. Comparison between the full periodic calculations and those for the isolated molecule shows that intermolecular interactions raise the methyl torsion transition energy by at least 8% and in some cases by more than 50%. The presence of more than one methyl group in the molecule generally raises the average torsion energy from the <100 cm–1 seen for single methyl groups to 150–200 cm–1.
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Chapter
The work in this chapter seeks to use the model employed in Chaps. 3 and 4 to investigate two polymorphic systems: HMX and FOX-7. The former contains two polymorphs that are well-known to exhibit markedly different impact sensitivity, while the impact sensitivity of the latter were measured here. The up-pumping model successfully captures the known sensitivity differences in the HMX polymorphs, and provides a rationale for the sensitivity measured for FOX-7 polymorphs.
Chapter
Many commonly used energetic materials (EM) are composed of organic molecules, with well-known examples including 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX), 2,4,6-trinitrotoluene (TNT) and triaminotrinitrobenzene (TATB). These compounds are typically based on similar structural moieties (explosophores), often −NO2 functionality, or numerous N–N, N–O or C–N bonds.
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Preprint
MIL-100 (Fe) is a highly porous metal-organic framework (MOF), considered as a promising carrier for drug delivery, and for gas separation and capture applications. However, this functional material suffers from elaborated and toxic synthesis that may hinder its biomedical use and large-scale production to afford commercial applications. Herein, we report a green mechanochemical water immersion approach to yield highly crystalline MIL100 (Fe) material. Subsequently, we have harnessed this strategy for facile fabrication of drug@MOF composite systems, comprising (guests) 5-fluorouracil, caffeine, or aspirin encapsulated in the pores of (host) MIL-100 (Fe). Inelastic neutron scattering was uniquely used to probe the guest host interactions arising from pore confinement of the drug molecules, giving additional insights into the reconstruction mechanism. Our results pave the way to the green production of MIL type materials and bespoke guest-encapsulated composites by minimizing the use of toxic chemicals, whilst enhancing energy efficiency and material's life cycle central to biotechnological applications.
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The organic acceptor, 7,7,8,8-tetracyanoquinodimethane (TCNQ), has been the subject of much research over the past few decades. Due to the π-conjugation of the quinodal structure, TCNQ as well as TCNQ based charge transfer compounds, exhibit some remarkable conducting properties. We present a study of the neutral TCNQ using inelastic neutron spectroscopy (INS) and show the first temperature dependent INS data collected on TCNQ allowing us to probe the temperature dependence of the low energy vibrational states, which have been shown to have an effect on charge delocalisation. Computational calculations have been used to help understand the data and the combination with the INS allows us to understand the phonon states. A complimentary experiment on deuterated TCNQ was also performed that allows a brief comparison of the isotopic substitution. This work utilises novel techniques to aid the understanding of the bulk properties of TCNQ in its neutral state that can be fed into work on other TCNQ based materials, including the exploration of deuteration as a technique to tune the properties of the parent compound.
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The vibrational properties of several High Entropy Alloy (HEA) based metal hydrides are investigated by inelastic neutron scattering (INS). HEAs have recently emerged as a new type of materials with a wide range of intriguing properties and potential applications such as hydrogen storage. The special properties of HEAs are believed to originate from the disordered lattice and internal strain that is introduced from the differences in atomic radii. This makes HEA hydrides provide an intriguing situation for the local H coordination, of several different transition metals. INS spectra were collected on a series of HEA-based metal hydrides starting with TiVNbHx and subsequently adding Zr and Hf to increase the atomic size mismatch. A general feature of the spectra are the optical peaks centered around an energy loss of 150 meV that can be attributed to hydrogen vibrations in a tetrahedral environment. Upon the addition of Zr and Hf, a shoulder appears on the optical peak at lower energy transfers that after comparison with in silico calculated INS spectra is indicative of hydrogen also occupying octahedral sites in the structure.
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The importance of electrically functional biomaterials is increasing as researchers explore ways to utilise them in novel sensing capacities. It has been recognised that for many of these materials the state of hydration is a key parameter that can heavily affect the conductivity, particularly those that rely upon ionic or proton transport as a key mechanism. However, thus far little attention has been paid to the nature of the water morphology in the hydrated state and the concomitant ionic conductivity. Presented here is an inelastic neutron scattering (INS) experiment on hydrated eumelanin, a model bioelectronic material, in order to investigate its 'water morphology'. We develop a rigorous new methodology for performing hydration dependent INS experiments. We also model the eumelanin dry spectra with a minimalist approach whereas for higher hydration levels we are able to obtain difference spectra to extract out the water scattering signal. A key result is that the physi-sorbed water structure within eumelanin is dominated by interfacial water with the number of water layers between 3-5, and no bulk water. We also detect for the first time, the potential signatures for proton cations, most likely the Zundel ion, within a biopolymer/water system. These new signatures may be general for soft proton ionomer systems, if the systems are comprised of only interfacial water within their structure. The nature of the water morphology opens up new questions about the potential ionic charge transport mechanisms within hydrated bioelectronics materials.
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Iridate pyrochlore oxides (Na,Ca) 2-x (Ir 2-y M y )O 6 ·nH 2 O (M = Sb, Zr, Ru, Rh) are studied as resilient electrocatalysts for the oxygen evolution reaction under acid conditions. The materials crystallise from aqueous solution under...
Chapter
This chapter explores the applications of a vibrational up-pumping model to predict the relative impact sensitivity of a series of simple azide-based energetic materials. Consideration for the decomposition of the explosophoric azido anion is presented, suggesting that motion along its bending normal mode can facilitate bond rupture. The relative rate of vibrational energy transfer into this bending motion is considered for each of the azide materials, and found to provide a good description for their relative impact sensitivity.
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The Mantid framework is a software solution developed for the analysis and visualization of neutron scattering and muon spin measurements. The framework is jointly developed by software engineers and scientists at the ISIS Neutron and Muon Facility and the Oak Ridge National Laboratory. The objectives, functionality and novel design aspects of Mantid are described.
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High-resolution inelastic neutron scattering and extensive first-principles calculations have been used to explore the low-temperature phase of the hybrid solar-cell material me-thylammonium lead iodide up to the well-known phase transition to the tetragonal phase at ca. 160 K. Contrary to original expectation, we find that the Pnma structure for this phase can only provide a qualitative description of the geometry and underlying motions of the organic cation. A substantial lowering of the local symmetry inside the perovskite cage leads to an improved atomis-tic model that can account for all available spectroscopic and thermodynamic data, both at low temperatures and in the vicinity of the aforementioned phase transition. Further and detailed analysis of the first-principles calculations reveals that large-amplitude distortions of the inorganic framework are driven by both zero-point-energy fluctuations and thermally activated cation motions. These effects are significant down to liquid-helium temperatures. For this important class of technological materials, this work brings to the fore the pressing need to bridge the gap between the long-range order seen by crystallographic methods and the local environment around the organic cation probed by neutron spectroscopy.
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High-resolution spectroscopic measurements using thermal and epithermal neutrons and first-principles calculations within the framework of density-functional theory are used to investigate the nuclear dynamics of light and heavy species in the metastable phase of caesium hydrogen sulfate. Within the generalised-gradient approximation, extensive calculations show that both 'standard' and 'hard' formulations of the Perdew-Burke-Ernzerhof functional supplemented by Tkatchenko-Scheffler dispersion corrections provide an excellent description of the known structure, underlying vibrational density of states, and nuclear momentum distributions measured at 10 and 300 K. Encouraged by the agreement between experiment and computational predictions, we provide a quantitative appraisal of the quantum contributions to nuclear motions in this solid acid. From this analysis, we find that only the heavier caesium atoms reach the classical limit at room temperature. Contrary to naïve expectation, sulfur exhibits a more pronounced quantum character relative to classical predictions than the lighter oxygen atom. We interpret this hitherto unexplored nuclear quantum effect as arising from the tighter binding environment of this species in this technologically relevant material.
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A combination of neutron-scattering experiments and first-principles calculations using density-functional theory have been performed to explore the structural and dynamical properties of the single-component organic ferroelectric croconic acid. Neutron diffraction and spectroscopy have been used to determine the location and underlying vibrational motions of the hydrogen ions within the crystalline lattice, respectively. On the computational front we find that dispersion corrections within the generalised-gradient approximation are essential to obtain a satisfactory crystal structure for this organic solid. Two distinct types of hydrogen ions in the crystal also have been identified, located at the ‘hinge’ and ‘terrace’ positions of a pleated, accordion-like structure. Phonon calculations and simulated neutron spectra show that the prominent doublet observed at ca. 1000 cm−1 arises from out-of-plane motions associated with these two types of hydrogen ions. Calculated Born-effective-charge tensors yield an anomalously high dynamic charge centered on the hydrogen ions at the hinges, a finding which serves to identify the primary motif underpinning ferroelectric behaviour in this novel material.
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Neutron spectroscopy is the only vibrational technique where the intensities can be calculated with reasonable accuracy. This method is applied here to benzene adsorbed in NaY zeolite. The force field of the adsorbed molecule has been refined directly to the observed neutron spectrum so that all the internal vibrational frequencies of benzene can be determined. The external modes of benzene relative to the cations were measured in the frequency range 10-100 cm(-1). This allows the sodium-benzene bond strength to be estimated.
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In Inelastic Neutron Scattering Spectroscopy, the neutron scattering intensity is plotted versus neutron energy loss giving a spectrum that looks like an infrared or a Raman spectrum. Unlike IR or Raman, INS does not have selection rules, i.e. all transitions are in principle observable. This particular characteristic makes INS a test bed for Density Functional Theory calculations of vibrational modes. aCLIMAX is the first user friendly program, within the Windows environment, that uses the output of normal modes to generate the calculated INS of the model molecule, making a lot easier to establish a connection between theory and experiment.Program summaryTitle of program: aCLIMAX 4.0.1Catalogue identifier: ADSWProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSWProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandOperating systems: Windows 95 onwards, except Windows ME where it does not workProgramming language used: Visual BasicMemory requirements: 64 MBNo. of processors: 1Has the code been parallelized: NoNo. of bytes in distributed program, including test data, etc.: 2 432 775No. of lines in distributed program, including test data, etc.: 17 998Distribution format: tar gzip fileNature of physical problem: Calculation of the Inelastic Neutron Scattering Spectra from DFT calculations of the vibrational density of states for molecules.Method of solution: INS spectral intensity calculated from normal modes analysis. Isolated molecule approximation.Typical time of running: From few seconds to few minutes depending on the size of the molecule.Unusual features of the program: Special care has to be taken in the case of computers that have different regional options than the English speaking countries, the decimal separator has to be set as “.” (dot) instead of the usual “,” (comma) that most countries use.