Measuring the Elasticity of Poly‐<scp>l</scp>‐Proline Helices with Terahertz Spectroscopy

Ruggiero, Michael T.; Šibík, Juraj; Orlando, Roberto; Zeitler, J. Axel; Korter, Timothy M.

doi:10.1002/anie.201602268

Cited by 55 publications

(37 citation statements)

References 55 publications

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“…Initially, the atomic positions and lattice parameters (taken from the experimental singlecrystal structure 32 ) were fully optimized with no constraints other than the space group symmetry of the solid, which has proven to produce excellent results for many organic and inorganic crystals. [24][25][26]35,[38][39][40]49,50 In the case of the simulated room temperature structure, the system was constrained to maintain the room-temperature volume, and all atomic positions and lattice vectors were allowed to relax within that constraint. Upon complete optimization, a vibrational analysis was performed by calculation of the second-derivative of the potential energy surface via a numerical finite difference scheme.…”

Section: ■ Methodsmentioning

confidence: 99%

Resolving the Origins of Crystalline Anharmonicity Using Terahertz Time-Domain Spectroscopy and ab Initio Simulations

Ruggiero

Zeitler

2016

J. Phys. Chem. B

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Anharmonicity has been shown to be an important piece of the fundamental framework that dictates numerous observable phenomena. In particular, anharmonicity is the driving force of vibrational relaxation processes, mechanisms that are integral to the proper function of numerous chemical processes. However, elucidating its origins has proven difficult due to experimental and theoretical challenges, specifically related to separating the anharmonic contributions from other unrelated effects. While no one technique is particularly suited for providing a complete picture of anharmonicity, by combining multiple complementary methods such a characterization can be made. In this study the role of individual atomic interactions on the anharmonic properties of crystalline purine, the building block of many DNA and RNA nucleobases, is studied by experimental terahertz time-domain spectroscopy and first-principles density functional theory (DFT) and ab initio molecular dynamics simulations (AIMD). In particular, the detailed vibrational information provided by the DFT calculations is used to interpret the atomic origins of anharmonic-related effects as determined by the AIMD calculations, which are in good agreement with the experimental data. The results highlight that anharmonicity is especially pronounced in the intermolecular interactions, particularly along the amine hydrogen bond coordinate, and yields valuable insight into what is similarly observed complex biosystems and crystalline solids.

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Section: ■ Methodsmentioning

confidence: 99%

Resolving the Origins of Crystalline Anharmonicity Using Terahertz Time-Domain Spectroscopy and ab Initio Simulations

Ruggiero

Zeitler

2016

J. Phys. Chem. B

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“…Low-frequency (terahertz) vibrational dynamics have been shown to be one of the major factors that dictate the properties of condensed phase materials, ranging from thermodynamic to mechanical phenomena [1,2]. Additionally, a number of recent investigations have suggested that terahertz motions, which often involve large amplitude displacements of entire molecules, play a vital role in the proper functioning of materials [3][4][5][6][7][8].…”

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confidence: 99%

Uncovering the Connection Between Low-Frequency Dynamics and Phase Transformation Phenomena in Molecular Solids

et al. 2018

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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.

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“…Even in the plastic crystal, in which the molecules generally move freely within their sites, there is a clear correlated rocking-type motion present. Interestingly, these oscillations have periods of about 1-2 ps, which is on the order of the period of terahertz vibrations (1 THz ¼ 10 12 Hz ¼ 1 ps). With the structures of the two forms known, a more rigorous analysis of the vibrational dynamics occurring within the solids can be performed.…”

Section: Structural Elucidation and Phase Transformation Pathwaymentioning

confidence: 98%

Predicting the structures and associated phase transition mechanisms in disordered crystals via a combination of experimental and theoretical methods

Ruggiero

Kölbel

et al. 2018

Faraday Discuss.

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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 pressuredependent properties to be understood within the framework of the potential energy hyper-surface structure.

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Measuring the Elasticity of Poly‐l‐Proline Helices with Terahertz Spectroscopy

Cited by 55 publications

References 55 publications

Resolving the Origins of Crystalline Anharmonicity Using Terahertz Time-Domain Spectroscopy and ab Initio Simulations

Resolving the Origins of Crystalline Anharmonicity Using Terahertz Time-Domain Spectroscopy and ab Initio Simulations

Uncovering the Connection Between Low-Frequency Dynamics and Phase Transformation Phenomena in Molecular Solids

Predicting the structures and associated phase transition mechanisms in disordered crystals via a combination of experimental and theoretical methods

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