Partial Vibrational Density Of States Research Articles

Pure and Sc-doped diopside (CaMgSi2O6) vibrational spectra: modelling and experiments.

We investigated the structure of pure and Sc-doped synthetic diopside (a monoclinic single-chain silicate nominally CaMgSi2O6); in Sc-doped diopside, Sc3+ substitutes Mg2+ in the structure and, to achieve charge balance, vacancies form at the expense of Ca2+. We compared the structure obtained from ab initio modelling techniques at the density functional theory (DFT) level with the structure solved by employing single crystal X-ray diffraction. Furthermore, we compared IR and Raman spectroscopy experiments with vibrational density of states (VDOS) calculated from the Fourier transform of the velocity autocorrelation function obtained using ab initio (DFT) molecular dynamics simulations. In this framework, we developed a computational tool to assign the vibrational mode associated with a specific frequency. This method consists of projecting velocities along a specific set of internal coordinates such as stretching or bending, in cases involving defects or vacancies, to calculate a partial VDOS (pVDOS) that takes into account only the vibrations associated with selected internal modes, aiding the interpretation of the total VDOS and the experimental spectra in a relevant way. The computed data were validated with the experiments and we observed that doping the diopside structure with Sc produces peak broadening and the occurrence of new peaks in the Raman spectra and that site vacancies are associated with the nearby Sc site. The present work constitutes an interesting starting point to exploit the calculated VDOS/pVDOS to characterize experimental vibrational spectra of complex systems containing local vacancies, substitutions or defects as the Sc-doped diopside.

Structural correlations of nitrogenase active sites using nuclear resonance vibrational spectroscopy and QM/MM calculations.

The biological conversion of N2 to NH3 is accomplished by the nitrogenase family, which is collectively comprised of three closely related but unique metalloenzymes. In the present study, we have employed a combination of the synchrotron-based technique of 57Fe nuclear resonance vibrational spectroscopy together with DFT-based quantum mechanics/molecular mechanics (QM/MM) calculations to probe the electronic structure and dynamics of the catalytic components of each of the three unique M N2ase enzymes (M = Mo, V, Fe) in both the presence (holo-) and absence (apo-) of the catalytic FeMco clusters (FeMoco, FeVco and FeFeco). The results described herein provide vibrational mode assignments for important fingerprint regions of the FeMco clusters, and demonstrate the sensitivity of the calculated partial vibrational density of states (PVDOS) to the geometric and electronic structures of these clusters. Furthermore, we discuss the challenges that are faced when employing NRVS to investigate large, multi-component metalloenzymatic systems, and outline the scope and limitations of current state-of-the-art theory in reproducing complex spectra.

Atomistic evidence of hydrodynamic heat transfer in nanowires

With wave-packet propagation simulations and heat flux estimation via molecular dynamics, we show that the heat flux radial distribution in silicon nanowires can be described by a mesoscopic model, the hydrodynamic heat equation. We observe Poiseuille like heat flux profile, that cannot be described by a simple kinetic model such as the Fuchs-Sondheimer model, in both pristine and core/shell nanowires. The addition of a shell does not change the shape of the radial heat flux distribution, but just modifies the maximum of the heat flux in the center of the nanowire. These results show that there is a heat flux depletion length for pristine or core shell nanowires, 1–2 nm away from the boundary of the crystalline part. The parameters of the mesoscopic model are discussed in terms of microscopic properties, including the phonon mean free path as function of frequency and the partial vibrational density of states in the different regions of the nanowire.

Vibrational properties of the mononuclear Fe[HBpz3]2 spin crossover complex

Within this work, we report the results of nuclear inelastic scattering experiments of the low-spin phase of the iron(II) mononuclear SCO complex Fe[HBpz3]2 and density functional theory based calculations performed on a model molecule of the complex. We show that the calculated partial density of vibrational states based on the structure of a single iron(II) center which is linked by three pyrazole rings to borat is in good accordance with the experimentally obtained 57Fe-pDOS and assign the molecular vibrations to the prominent optical phonons.

Exploration of iron ligand modes in dimeric iron (II) complexes by nuclear resonance scattering

The vibronic properties of two dimeric iron (II) high-spin complexes [5CpFeX]2 (5Cp = Pentaisopropyl-cyclopentadienyl, X = OH-(1), Br-(2)) have been studied using nuclear inelastic scattering (NIS). In order to assign the experimentally observed bands to the particular modes, theoretical calculations using density functional theory (DFT) have been performed based on the structural data obtained by X-ray crystallography. The calculated partial density of vibrational states (pDOS) reproduces the experimental data. Thus, we were able to assign almost each of the experimentally observed NIS bands to their corresponding molecular vibrational modes.

Preferential heating of aqueous amine solutions using infrared radiation at selected vibrational frequencies: A molecular dynamics study.

A recent CO2 capture experiment suggests that microwaves might be beneficial for regeneration of aqueous amine solutions due to both thermal and nonthermal effects [S. J. McGurk et al., Appl. Energy 192, 126 (2017)]. We use classical molecular dynamics to simulate heating of aqueous amine solutions using electromagnetic radiation with different frequencies in both microwave and infrared regions. The infrared frequencies were selected based on the partial vibrational density of states of water and amine. Unlike the microwave case, we found that preferential heating of water or amine can be achieved using their relevant vibrational frequencies in the infrared region, suggesting that microwave heating is not an optimal choice for an efficient amine regeneration reported in a recent carbon capture experiment. Interestingly, only flexible water models augmented with an anharmonic O-H bond stretching potential were able to quantitatively predict the expected differential heating profiles of systems involving water.

Understanding the interfacial interactions of bioinspired chitosan-calcite nanocomposites by first principles molecular dynamics simulations and experimental FT-IR spectroscopy

The interfacial structures and bonding mechanism of the adsorption of chitosan monomers (GlcN and GlcNAc) on calcite (104) surface are investigated using first principles molecular dynamics simulations. It is revealed that the strong coordination CaO bonds are formed between five-fold coordinated Ca atoms on calcite surface and O atoms of hydroxyl groups (OH) and acetyl groups of chitosan in the chitosan-calcite nanocomposites, improving the chemical compatibility between organic and inorganic phases at the interface in the natural occurring nacre. Although, the presence of interfacial hydrogen bonds is also confirmed by analyzing the valence electron density difference in terms of induced dipole, the evolution of the equilibrium adsorption geometry is found to be mainly governed interfacial CaO coordination bonds. The amide group (NH2) of chitosan binds with calcite at the interface mainly through the formation of weak hydrogen bond. The predicted interfacial electronic structure can be either conductive (GlcNAc) or insulating (GlcN). The frequencies of the characteristic peaks in the calculated total and partial vibrational densities of states of GlcN/calcite systems are found to be in agreement with the FT-IR spectrum of the experimentally prepared chitosan-calcite nanocomposites, crucially validating the modelling structures and computational methodology employed in current work. Theoretical results strongly indicate that the peculiar adsorption in FT-IR spectrum at 2500 cm−1 is related to the presence of free GlcN molecule due to the hydrolysis of chitosan in aqueous solution.

Anisotropy of the proton kinetic energy in ice Ih

The partial vibrational density of states (pVDOS) of ice Ih, as simulated by first principle modeling based on density functional theory (DFT), is utilized for computing the Cartesian components of the proton and oxygen quantum kinetic energies, Ke(H) and Ke(O) respectively, along and perpendicular to the hydrogen bonds. The DFT method was found to yield better agreement with deep inelastic neutron scattering (DINS) measurements than the semi empirical (SE) calculations. The advantage of using the DFT method is to enable us to resolve the external and internal phonon bands of the Cartesian projections of the pVDOS, and hence those of the lattice and vibrational components of Ke(H). We show that a pVDOS analysis is a valuable tool in testing scattering results of complex systems and suggest its potential to explore competing quantum effects, e.g. on Ke(H) across phase transitions in water.

Partial vibrational density of states for amorphous solids from inelastic neutron scattering

Partial vibrational density of states for amorphous solids from inelastic neutron scattering

Nuclear inelastic scattering studies of a 1D- polynuclear spin crossover complex of Fe(II) urea-triazoles

The partial density of vibrational states (pDOS) of the low-spin isomer of the tosylate salt of [Fe{(N-Propyl)-N′-(1,2,4-triazole-4-yl-urea)}3]2+ was determined by nuclear inelastic scattering experiments performed at 8 K. The pDOS features a rich band structure from 320 to 500 cm−1, characteristic of the low spin state of the complex. Density functional theory calculations (B3LYP/CEP-31G) were used to assign molecular modes to the experimentally observed peak in the pDOS.

Phonon excitations in a single crystal Mg85Zn6Y9 with a synchronized long-period stacking ordered phase

Inelastic X-ray scattering (IXS) experiments were carried out at room temperature at BL35XU of the SPring-8 on a single crystal Mg85Zn6Y9 alloy with a synchronized long-period stacking ordered (LPSO) phase of purely 18R type. The IXS measurements were carried out in both the longitudinal and transverse directions along the Γ-K and Γ-M (momentum vector q⊥ lattice axis c), and Γ-A (q∥c) directions for the energy transfers ω below 40 meV. Peaks arising from longitudinal and transverse acoustic (LA and TA) modes were clearly observed in the IXS spectra. The dispersion relations of the LA and TA modes in the Mg85Zn6Y9 LPSO alloy are mostly similar to those of previous INS data on single crystal pure Mg. New impurity-derived dispersion-less excitation modes are observed along all of the crystal directions at about 5, 10, and 17 meV. Partial vibrational density of states (vDOS) was obtained using an abinitio molecular dynamics simulation, and it was found that the ∼10 meV peak mainly originates from the phonon excitations inside the L12-type Zn6Y8 clusters and the ∼17 meV peak from those between the cluster and the host Mg atoms, and a small shoulder at 5 meV consists of motions of all the elements. These findings clarify that the dispersion-less modes mainly correspond to localized stretching and twisting modes around the impurity clusters in the LPSO alloys.

Anisotropy of the proton kinetic energy in CsH2PO4 and KH2PO4

The strong anisotropy of the proton mean kinetic energy, Ke(H), in a single crystal of KH2PO4 (KDP), measured by deep inelastic neutron scattering (DINS), is compared with that calculated for its Cs analogue, CsH2PO4 (CDP) in the ferroelectric (FE) and paraelectric (PE) phases. Empirical lattice dynamics (LD) calculations were used to simulate the partial vibrational density of states shared by the protons (H-VDOS), from which Ke(H) values were deduced. Good agreement was found between the measured and calculated Ke(H) values of the two samples despite the different hydrogen bond dynamics. However, the directional components of Ke(H) in the two samples were quite different. In both cases, the Ke(H) tensor is nearly an ellipsoid of rotation: in KDP the shape is oblate around the major axis while being prolate in CDP. By resolving the directional Ke(H) values of the two non-equivalent protons of CDP, a possible signature of competing quantum effects is indicated.

Nuclear inelastic scattering at the diiron center of ribonucleotide reductase from Escherichia coli

The enzyme ribonucleotide reductase R2 catalyzes an important step in the synthesis of the building blocks of DNA, and harbors a dinuclear iron center required for activity. Not only the iron valence states but also the protonation of the iron ligands govern the enzymatic activity of the enzyme. We have performed Nuclear Inelastic Scattering (NIS) experiments on the 57Fe reconstituted ribonucleotide reductase R2 subunit from Escherichia coli (Ec R2a). Accompanying Mossbauer spectroscopic investigations show that the partial density of vibrational states (pDOS) of the 57Fe reconstituted Ec R2a sample contained contributions from both 57Fe-Ec R2a protein as well as unspecifically bound 57Fe. Subtraction of a featureless pDOS as obtained from protein-coated iron oxide particles allowed modeling of the contribution of non-specifically bound iron and thus the pDOS of 57Fe-Ec R2a could be obtained. Quantum-mechanics/molecular-mechanics (QM/MM) calculations of the whole 57Fe-Ec R2a protein with variations of the cofactor protonation were performed in order to assign characteristic bands to their corresponding molecular vibrational modes.

Operando Phonon Studies of the Protonation Mechanism in Highly Active Hydrogen Evolution Reaction Pentlandite Catalysts.

Synthetic pentlandite (Fe4.5Ni4.5S8) is a promising electrocatalyst for hydrogen evolution, demonstrating high current densities, low overpotential, and remarkable stability in bulk form. The depletion of sulfur from the surface of this catalyst during the electrochemical reaction has been proposed to be beneficial for its catalytic performance, but the role of sulfur vacancies and the mechanism determining the reaction kinetics are still unknown. We have performed electrochemical operando studies of the vibrational dynamics of pentlandite under hydrogen evolution reaction conditions using 57Fe nuclear resonant inelastic X-ray scattering. Comparing the measured Fe partial vibrational density of states with density functional theory calculations, we have demonstrated that hydrogen atoms preferentially occupy substitutional positions replacing pre-existing sulfur vacancies. Once all vacancies are filled, the protonation proceeds interstitially, which slows down the reaction. Our results highlight the beneficial role of sulfur vacancies in the electrocatalytic performance of pentlandite and give insights into the hydrogen adsorption mechanism during the reaction.

Vibrational properties of Cu3XY4 sulvanites (X = Nb, Ta, and V; and Y = S, and Se) by ab initio molecular dynamics

In this work, we present a structural and dynamic characterisation of six different types of sulvanites Cu3 X Y 4 with X = Nb, V and Ta, and Y = S and Se. These materials have been the subject of intense study in recent times primarily as potential candidates for solar cell devices, as well as for their enhanced opto-electrical properties. Here, by means of first-principles calculations, we study the structural and dynamic behaviour of these materials at different temperatures, which is important for use of these materials in high-temperature conditions. In this work the dynamic and structural properties are studied using the Density Functional Theory technique. The simulations were performed at four different temperatures, ranging from room temperature to ~1500 K. By using first-principles molecular dynamics in the microcanonical ensemble, we are able to determine the vibrational spectra of these sulvanites. With this information we report for the first time the partial vibrational density of states of these structures at different temperatures. With these results we determine the vibrational properties of the basic building blocks of those sulvanites and their dynamic behaviour under temperature effects. We also show that the building blocks that which make up these structures, remain stable as the temperature increases.

Finite-size effects on the lattice dynamics in spin crossover nanomaterials. I. Nuclear inelastic scattering investigation

We report the investigation of the size evolution of lattice dynamics in spin crossover coordination nanoparticles of $\mathrm{[}\mathrm{Fe}(\mathrm{pyrazine})(\mathrm{Ni}{(\mathrm{CN})}_{4})]$ through nuclear inelastic scattering (NIS) measurements. Vibrational properties in these bistable molecular materials are of paramount importance and NIS permits access to the partial vibrational density of states in both spin states [high spin (HS) and low spin (LS)] from which thermodynamical and mechanical properties can be extracted. We show that the size reduction leads to the presence of inactive metal centers with the coexistence of HS and LS vibrational modes. The confinement effect has only weak impact on the vibrational properties of nanoparticles, especially on the optical modes which remain almost unchanged. On the other hand, the acoustic modes are much more affected which results in the increase of the vibrational entropy and also the Debye sound velocity in the smallest particles $(l10$ nm) in both spin states. This stiffening may be due to the elastic surface stress exerted by the external environment. An evidence of the influence of the host matrix on the vibrational properties of the nanoparticles is also highlighted through the matrix dependence of the sound velocity.

Quantum behavior of water nano-confined in beryl.

The proton mean kinetic energy, Ke(H), of water confined in nanocavities of beryl (Be3Al2Si6O18) at 5 K was obtained by simulating the partial vibrational density of states from density functional theory based first-principles calculations. The result, Ke(H) = 104.4 meV, is in remarkable agreement with the 5 K deep inelastic neutron scattering (DINS) measured value of 105 meV. This is in fact the first successful calculation that reproduces an anomalous DINS value regarding Ke(H) in nano-confined water. The calculation indicates that the vibrational states of the proton of the nano-confined water molecule distribute much differently than in ordinary H2O phases, most probably due to coupling with lattice modes of the hosting beryl nano-cage. These findings may be viewed as a promising step towards the resolution of the DINS controversial measurements on other H2O nano-confining systems, e.g., H2O confined in single and double walled carbon nanotubes.

On the Atomic Kinetic Energies in Ceramic Oxides

We calculated the mean atomic kinetic energy, , of the X atom (X = Si, Ti, Hf, O) in some ceramic oxides, SiO2, TiO2 and HfO2 using the published partial vibrational density of states (PVDOS). These were simulated by means of lattice dynamics, molecular dynamics and density functional theory. The predicted values are compared to those recently obtained by electron Compton scattering (ECS), with an overall good agreement of ~4%. In accord with calculations, the ECS measurements reveal a small, but detectable, dependence of on the fine structural details of the oxide, e.g. whether it is in a crystalline or amorphous form, and whether it exhibits surface or bulk characteristics. This study illustrates the limitations and the potential of PVDOS simulations in predicting experimental atomic kinetic energies, and can be viewed as a promising approach for elucidating valuable structural and dynamical information of ceramic oxides and other materials.

First-principles calculations of phonons and Raman spectra in the Hg3Te2Cl2 crystals

This paper presents a systematic first-principles study of phonons and Raman spectra of cubic Hg3Te2Cl2 within a framework of DFT in the GGA/PBE approximation. The phonon dispersion, total and partial density of vibrational states for Hg3Te2Cl2 crystals are analyzed. The identification of the vibrational modes at the Brillouin zone center is conducted and discussed in details. The first-principles calculated Raman-active phonon frequencies and simulated Raman spectra are compared with experimental data. The assignment of the phonon lines to define atomic vibrations was made on the basis of their symmetries in close comparison with results of lattice-dynamical calculations. Satisfactory agreement is obtained with experimental mode frequencies.

Simultaneous characterization of protein coated iron oxide nanoparticles with nuclear inelastic scattering and atomic force microscopy

Bovine serum albumin coated magnetic iron oxide nanoparticles (IONPs), which were synthesized using a co-precipitation method with 57Fe have been subject to a combined study using atomic force microscopy (AFM) and nuclear inelastic scattering (NIS). The obtained partial density of vibrational states (pDOS) shows evidence for lattice stiffening and a pronounced mode at 23 meV compared to thin film magnetite at room temperature.