Porous materials, particularly metal-organic frameworks (MOFs), hold great promise for advanced applications. MIL-53(Al) is an exceptionally well-studied MOF that exhibits a phase transition upon guest captureâin this case, waterâresulting in a dramatic change in the pore volume. Despite extensive studies, the structure of the water-loaded narrow-pore phase, MIL-53(Al)-np, remains controversial, particularly with respect to the positions of the adsorbed water molecules. We use terahertz spectroscopy, coupled with powder X-ray diffraction and density functional theory simulations, to unambiguously resolve this controversy. We show that the low-frequency (<100 cm-1) vibrational spectrum depends on weak long-range forces that are extremely sensitive to the orientation of the adsorbed water molecules. This enables definitively determining the correct structure of MIL-53(Al)-np while highlighting the extreme sensitivity of terahertz spectroscopy to bulk structure, suggesting its potential as a robust complement to X-ray diffraction for precise characterization of host-guest complexes.
Terahertz spectroscopy has proved to be an essential tool for the study of condensed phase materials. Terahertz spectroscopy probes the low-frequency vibrational dynamics of atoms and molecules, usually in the condensed phase. These nuclear dynamics, which typically involve displacements of entire molecules, have been linked to bulk phenomena ranging from phase transformations to semiconducting efficiency. The terahertz region of the electromagnetic spectrum has historically been referred to as the 'terahertz gap', but this is a misnomer, as there exist a multitude of methods for accessing terahertz frequencies, and now there are cost-effective instruments that have made terahertz studies much more user-friendly. This Review highlights some of the most exciting applications of terahertz vibrational spectroscopy so far, and provides an in-depth overview of the methods of this technique and its utility to the study of the chemical sciences.
Terahertz Spectroscopy , Vibration
The solvation shell is essential for the folding and function of proteins, but how it contributes to protein misfolding and aggregation has still to be elucidated. We show that the mobility of solvation shell H2 O molecules influences the aggregation rate of the amyloid protein α-synuclein (αSyn), a protein associated with Parkinson's disease. When the mobility of H2 O within the solvation shell is reduced by the presence of NaCl, αSyn aggregation rate increases. Conversely, in the presence CsI the mobility of the solvation shell is increased and αSyn aggregation is reduced. Changing the solvent from H2 O to D2 O leads to increased aggregation rates, indicating a solvent driven effect. We show the increased aggregation rate is not directly due to a change in the structural conformations of αSyn, it is also influenced by a reduction in both the H2 O mobility and αSyn mobility. We propose that reduced mobility of αSyn contributes to increased aggregation by promoting intermolecular interactions.
Parkinson Disease , alpha-Synuclein , Humans , alpha-Synuclein/chemistry , Water , Solvents
The solvation shell is essential for the folding and function of proteins, but how it contributes to protein misfolding and aggregation has still to be elucidated. We show that the mobility of solvation shell H2O molecules influences the aggregation rate of the amyloid protein α-synuclein (αSyn), a protein associated with Parkinson's disease. When the mobility of H2O within the solvation shell is reduced by the presence of NaCl, αSyn aggregation rate increases. Conversely, in the presence CsI the mobility of the solvation shell is increased and αSyn aggregation is reduced. Changing the solvent from H2O to D2O leads to increased aggregation rates, indicating a solvent driven effect. We show the increased aggregation rate is not directly due to a change in the structural conformations of αSyn, it is also influenced by a reduction in both the H2O mobility and αSyn mobility. We propose that reduced mobility of αSyn contributes to increased aggregation by promoting intermolecular interactions.
Zr-oxide secondary building units construct metal-organic framework (MOF) materials with excellent gas adsorption properties and high mechanical, thermal, and chemical stability. These attributes have led Zr-oxide MOFs to be well-recognized for a wide range of applications, including gas storage and separation, catalysis, as well as healthcare domain. Here, we report structure search methods within the Cambridge Structural Database (CSD) to create a curated subset of 102 Zr-oxide MOFs synthesized to date, bringing a unique record for all researchers working in this area. For the identified structures, we manually corrected the proton topology of hydroxyl and water molecules on the Zr-oxide nodes and characterized their textural properties, Brunauer-Emmett-Teller (BET) area, and topology. Importantly, we performed systematic periodic density functional theory (DFT) calculations comparing 25 different combinations of basis sets and functionals to calculate framework partial atomic charges for use in gas adsorption simulations. Through experimental verification of CO2 adsorption in selected Zr-oxide MOFs, we demonstrate the sensitivity of CO2 adsorption predictions at the Henry's regime to the choice of the DFT method for partial charge calculations. We characterized Zr-MOFs for their CO2 adsorption performance via high-throughput grand canonical Monte Carlo (GCMC) simulations and revealed how the chemistry of the Zr-oxide node could have a significant impact on CO2 uptake predictions. We found that the maximum CO2 uptake is obtained for structures with the heat of adsorption values >25 kJ/mol and the largest cavity diameters of ca. 6-7 Å. Finally, we introduced augmented reality (AR) visualizations as a means to bring adsorption phenomena alive in porous adsorbents and to dynamically explore gas adsorption sites in MOFs.
The role of low-frequency (terahertz) vibrational motions on charge carrier dynamics in organic semiconductors (OSCs) is becoming well-known, and efforts are underway to rationally design new materials to mitigate these detrimental effects. However, most efforts have focused on stabilizing the fused-ring semiconducting 'core', often by functionalizing with various side-groups, yet questions regarding the role of such modifications on electron-phonon couplings are still outstanding. In this work, the influence of thiophene rings σ-bonded directly to the π-conjugated cores is explored. The manner in which these groups alter low-frequency vibrational, and resulting electronic, dynamics is quantified using a theoretical approach employing fully-periodic density functional theory (DFT) simulations. Ultimately, these results showcase how the equilibrium geometry and corresponding electronic structure are directly related to detrimental electron-phonon coupling, which have important implications for the design of improved organic optoelectronic materials.
The anharmonicity of O-H stretching vibrations of water ice is characterized by use of a periodic implementation of the vibrational self-consistent field (VSCF) and vibrational configuration interaction (VCI) methods, which take phonon-phonon couplings explicitly into account through numerical evaluation of high-order terms of the nuclear potential. The low-temperature, proton-ordered phase of water ice (namely, ice XI) is investigated. The net effect of a coupled anharmonic treatment of stretching modes is not just a rigid blue-shift of the respective harmonic spectral frequencies but rather a complex change of their relative spectral positions, which cannot be captured by simple scaling strategies based on harmonic calculations. The adopted techniques allow for a hierarchical treatment of anharmonic terms of the nuclear potential, which is key to an effective identification of leading factors. We show that the anharmonic independent-mode approximationâonly describing the "intrinsic anharmonicity" of the O-H stretchesâis unable to capture the correct physics, and that couplings among O-H stretches must be described. Inspection of harmonic normal coordinates allows identification of specific features of the O-H stretching motions which most likely enable strong mode-mode couplings. Finally, by coupling O-H stretches to all other possible modes of ice XI (THz collective vibrations, molecular librations, bendings), we identify specific types of motion which significantly affect O-H stretching states: in particular, molecular librations are found to affect the stretching states more than molecular bendings.
Ice , Vibration , Models, Molecular , Motion , Protons
In this report, the strong-dependence of low-frequency (terahertz) vibrational dynamics on weak and long-range forces in crystals is leveraged to determine the bulk magnetic configuration of iron phosphate - a promising material for cathodes in lithium ion batteries. We demonstrate that terahertz time-domain spectroscopy - coupled with quantum mechanical simulations - can discern between various spin configurations in FePO4. Furthermore, the results of this work unambiguously show that the well-accepted space group symmetry for FePO4 is incorrect, and the low-frequency spectroscopic measurements provide a clearer picture of the correct structure over the gold-standard of X-ray diffraction. This work opens the door for characterizing, predicting, and interpreting crystalline magnetic ordering using low-frequency vibrational spectroscopy.
Terahertz vibrational spectroscopy has emerged as a powerful spectroscopic technique, providing valuable information regarding long-range interactions - and associated collective dynamics - occurring in solids. However, the terahertz sciences are relatively nascent, and there have been significant advances over the last several decades that have profoundly influenced the interpretation and assignment of experimental terahertz spectra. Specifically, because there do not exist any functional group or material-specific terahertz transitions, it is not possible to interpret experimental spectra without additional analysis, specifically, computational simulations. Over the years simulations utilizing periodic boundary conditions have proven to be most successful for reproducing experimental terahertz dynamics, due to the ability of the calculations to accurately take long-range forces into account. On the other hand, there are numerous reports in the literature that utilize gas phase cluster geometries, to varying levels of apparent success. This perspective will provide a concise introduction into the terahertz sciences, specifically terahertz spectroscopy, followed by an evaluation of gas phase and periodic simulations for the assignment of crystalline terahertz spectra, highlighting potential pitfalls and good practice for future endeavors.
Fluorescence in biological systems is usually associated with the presence of aromatic groups. Here, by employing a combined experimental and computational approach, we show that specific hydrogen bond networks can significantly affect fluorescence. In particular, we reveal that the single amino acid L-glutamine, by undergoing a chemical transformation leading to the formation of a short hydrogen bond, displays optical properties that are significantly enhanced compared with L-glutamine itself. Ab initio molecular dynamics simulations highlight that these short hydrogen bonds prevent the appearance of a conical intersection between the excited and the ground states and thereby significantly decrease nonradiative transition probabilities. Our findings open the door to the design of new photoactive materials with biophotonic applications.
Ammonia/chemistry , Glutamine/chemistry , Peptides/chemistry , Density Functional Theory , Fluorescence , Humans , Hydrogen Bonding , Molecular Dynamics Simulation , Optics and Photonics/methods
Molecular crystals are increasingly being used for advanced applications, ranging from pharmaceutics to organic electronics, with their utility dictated by a combination of their three-dimensional structures and molecular dynamics-with anharmonicity in the low-frequency vibrations crucial to numerous bulk phenomena. Through the use of temperature-dependent x-ray diffraction and terahertz time-domain spectroscopy, the structures and dynamics of a pair of isomeric molecular crystals exhibiting nearly free rotation of a CF_{3} functional group at ambient conditions are fully characterized. Using a recently developed solid-state anharmonic vibrational correction, and applying it to a molecular crystal for the first time, the temperature-dependent spatial displacements of atoms along particular terahertz modes are obtained, and are found to be in excellent agreement with the experimental observations, including the assignment of a previously unexplained absorption feature in the low-frequency spectrum of one of the solids.
Terahertz (THz) spectroscopy was used to observe adsorbed water structure and dynamics within polymer films, ultimately providing a strong rationale for the observed rates of water desorption. The THz absorption spectra of nylon-6 films undergo drastic changes during the hydration and drying processes. Additionally, the structural change from γ to α crystals, induced by the hydration, was observed by the characteristic band of α-nylon-6 at 6.5 THz. Importantly, the THz spectra of adsorbed water, as well as deuterated water, within in the nylon films were observed by the continuous measurement of α-nylon during dehydration. The difference spectra clearly show three absorption bands of water molecules named Peaks I-III, which behave differently between the H2O and D2O materials. The spectra were assigned using a combination of ab initio molecular dynamics simulations and solid-state density functional theory calculations and were compared to previous spectral assignments of bulk water. The results show that the inclusion of H2O and D2O into polymer films results in a distinct set of spectral features that, while similar in frequencies to the dynamics of bulk water, represent significantly different motions owing to the unique chemical environment within the material. These results highlight the significant utility of using THz spectroscopy to study the hydration dynamics and spectral signatures of bound water in this important class of materials.
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.
In this study the glass transition temperatures (Tgα and Tgß) in mesoporous silica-based amorphous drugs were characterized. For this purpose, mesoporous silica Parteck SLC (MPS) was loaded with the drugs ibuprofen and carvedilol, either below, at, or above the monomolecular drug loading capacities, i.e. the concentration at which the entire MPS surface is covered with a monolayer of drug molecules. The resulting amorphous forms were analysed using X-ray powder diffraction and the thermal behaviour was characterised with differential scanning calorimetry (DSC) and dynamic mechanical analysis (DMA). The drug monolayer did not contribute to the thermal signal in DSC. Using DMA however, it could be shown that the monolayer indeed exhibited a very weak Tgα, and that the temperature range of this transition did not differ from that of the quench cooled amorphous drugs. Theoretical ab initio molecular dynamics simulations revealed that the nature of hydrogen bonding geometry of the functional groups interacting with the MPS surface were similar to that of the respective crystalline drugs, which results in restricted molecular motions for those functional groups. On the other hand, the non-interacting parts of the molecules exhibited molecular motions similar to what is observed in pure amorphous drugs. As a result of the interactions of the monolayer with the MPS surface, the monomolecular drug layer did not reveal a Tgß. However, a Tgß was found at any drug-MPS ratios above the monomolecular drug loading capacity as a result of the excess drug which forms a "true" amorphous phase. Overall, this study demonstrated that drug molecules forming an amorphous monolayer on the surfaces of a mesoporous silica particle, even though they are restricted in their mobility, exhibit a Tgα, but lack a Tgß, whereas any excess drug confined in the MPS pores showed similar properties as the pure amorphous drug. These findings will help to increase the overall understanding of drug loaded MS systems, including their physical stability as well as release properties.
Glass/chemistry , Silicon Dioxide/chemistry , Transition Temperature , Calorimetry, Differential Scanning , Carvedilol/chemistry , Drug Liberation , Drug Stability , Ibuprofen/chemistry , Molecular Dynamics Simulation
We measured crystalline (C-form) saturated fatty acids with even carbon numbers ranging from 12 to 20 using temperature dependent terahertz time-domain spectroscopy (THz-TDS). Absorption features between 0.5 and 3 THz were identified at temperatures from 96 K to 293 K, and a systematic red-shift was obvserved with the increasing carbon chain length. The origins of these absorption bands were uncovered using state-of-the-art ab initio density functional theory (DFT) calculations. Similar vibrational motions in the absorption bands of the different materials highlight the unique role that THz-TDS has for probing weak non-covalent interactions in these materials. Our results showcase the utility of the terahertz region, which is beyond the scope of related vibrational techniques, providing direct evidence of the effect of chain length on the intermolecular interactions of these molecules.
Pure metal-organic framework (MOF) layers deposited on porous supports are important candidates for molecular sieving membranes, but their performance usually deviates from theoretical estimations. Here, we combine step-wise scanning electron microscopy imaging, time-resolved synchrotron X-ray scattering, terahertz infrared spectroscopy, and density functional theory calculation to investigate the ZIF-8 membrane formation on two types (polydopamine and TiO2) of functionalized porous supports. Though molecular sieving of ZIF-8 membranes for smaller gases (He, H2, and CO2) can be achieved with both types of functionalized supports, we unravel that the strong interaction between MOF and polydopamine can disrupt the formation of "perfect" MOF crystals at the interface, leading to a "contracted" MOF structure with partially uncoordinated imidazolate ligands. This further affects the low-frequency dynamical parameters of the framework and inhibits the effective seeded growth. Eventually, it leads to an unexpected loss of selectivity for the bulkier gases (N2 and CH4) for ZIF-8 on polydopamine-functionalized supports. This work links the dynamical aspects of MOFs with their gas transport behavior and highlights the importance of regulating the interfacial weak forces to preserve the ideal molecular sieving efficiency of MOF membranes, which also provides guidance for defect engineering of MOF film fabrication for sensing and electronic devices beyond membranes.
Disordered materials make up a large proportion of condensed phase systems, but the difficulties in describing their structures and molecular dynamics limit their potential applications. Disordered crystalline systems, also known as plastic crystals, offer a unique perspective into these factors because the systems retain a degree of crystallinity, reducing the degrees of freedom that must be explored when interpreting the results. However, while disordered crystals do diffract X-rays, it is difficult to fully resolve meaningful crystalline structures, with the best scenario resulting in lattice parameters. In this study, we use a combination of experimental terahertz time-domain spectroscopy, and theoretical solid-state ab initio density functional theory and molecular dynamics simulations to fully elucidate the structures and associated dynamics of organic molecular solids. The results highlight that this combination provides a complete description of the energetic and mechanistic pathways involved in the formation of disordered crystals, and highlights the importance of low-frequency dynamics in their properties. Finally, with structures fully determined and validated by the experimental results, recent progress into anharmonic calculations, namely the quasi-harmonic approximation method, enables full temperature and pressure-dependent properties to be understood within the framework of the potential energy hyper-surface structure.
The low-frequency motions of molecules in the condensed phase have been shown to be vital to a large number of physical properties and processes. However, in the case of disordered systems, it is often difficult to elucidate the atomic-level details surrounding these phenomena. In this work, we have performed an extensive experimental and computational study on the molecular solid camphor, which exhibits a rich and complex structure-dynamics relationship, and undergoes an order-disorder transition near ambient conditions. The combination of x-ray diffraction, variable temperature and pressure terahertz time-domain spectroscopy, ab initio molecular dynamics, and periodic density functional theory calculations enables a complete picture of the phase transition to be obtained, inclusive of mechanistic, structural, and thermodynamic phenomena. Additionally, the low-frequency vibrations of a disordered solid are characterized for the first time with atomic-level precision, uncovering a clear link between such motions and the phase transformation. Overall, this combination of methods allows for significant details to be obtained for disordered solids and the associated transformations, providing a framework that can be directly applied for a wide range of similar systems.
In ZIF-8 and its cobalt analogue ZIF-67, the imidazolate methyl-groups, which point directly into the void space, have been shown to freely rotate - even down to cryogenic temperatures. Using a combination of experimental terahertz time-domain spectroscopy, low-frequency Raman spectroscopy, and state-of-the-art ab initio simulations, the methyl-rotor dynamics in ZIF-8 and ZIF-67 are fully characterized within the context of a quantum-mechanical hindered-rotor model. The results lend insight into the fundamental origins of the experimentally observed methyl-rotor dynamics, and provide valuable insight into the nature of the weak interactions present within this important class of materials.
