The effect of the flexibility of hydrogen bonding network on low-frequency motions of amino acids. Evidence from Terahertz spectroscopy and DFT calculations

Li, Yin; Lukács, András; Bordács, S.; Móczár, János; Nyitrai, Miklós; Hebling, J.

doi:10.1016/j.saa.2017.09.035

Cited by 19 publications

(7 citation statements)

References 34 publications

(48 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…While introducing the use of the analytical response scheme by Gonze and Baroni [37][38][39][52][53][54][55], this paper provides a proven numerical recipe for an accurate modeling of low-wavenumber phonon frequencies. This strategy has been followed with a number of examples presented in the literature, using CASTEP [30][31][32][33][105][106][107][108][109], QUAN-TUM ESPRESSO [106,[110][111][112][113][114], ABINIT [115][116][117], or VASP [118,119], and has been used in the present study. Instead of advocating any of the presented strategies, we further highlight the main differences and limitations of each approach as both have their pros and cons.…”

Section: Current Trends and Advances In Modelling Of Terahertz Spectramentioning

confidence: 99%

Vibrational Response of Felodipine in the THz Domain: Optical and Neutron Spectroscopy Versus Plane-Wave DFT Modeling

Łuczyńska

Drużbicki

Runka

et al. 2019

J Infrared Milli Terahz Waves

View full text Add to dashboard Cite

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

show abstract

Section: Current Trends and Advances In Modelling Of Terahertz Spectramentioning

confidence: 99%

Vibrational Response of Felodipine in the THz Domain: Optical and Neutron Spectroscopy Versus Plane-Wave DFT Modeling

Łuczyńska

Drużbicki

Runka

et al. 2019

J Infrared Milli Terahz Waves

View full text Add to dashboard Cite

show abstract

“…This is because the experiments were performed at 294 K while the simulations are performed at 0 K, which leads to the shift to higher-frequencies upon cooling. The linear scaling factors were adjusted to all vibrational modes of C and C-MH, with scaling factors of 0.88 and 0.85, respectively 46,47 . The reason for the more scaled factor of C-MH might be the vibrational anharmonicity which plays a significant role in H 2 O-containing molecular crystal 48 .…”

Section: Results Thz Absorption Spectra Of C and C-mh The Experimentmentioning

confidence: 99%

Transformation of terahertz vibrational modes of cytosine under hydration

Lee

Cheon

Jeong

et al. 2020

Sci Rep

View full text Add to dashboard Cite

Cytosine and cytosine monohydrate are representative biomolecules for investigating the effect of hydrogen bonds in deoxyribonucleic acid. to better understand intermolecular interactions, such as hydrogen bonds, between nucleobases it is necessary to identify the low-frequency vibrational modes associated with intermolecular interactions and crystalline structures. in this study, we investigated the characteristic low-frequency vibrational modes of cytosine and cytosine monohydrate using terahertz time-domain spectroscopy (tHz-tDS). the crystal geometry was obtained by the powder X-ray diffraction technique. The optimized atomic positions and the normal modes in the terahertz region were calculated using density functional theory (Dft), which agreed well with the experimental results. We found that overall terahertz absorption peaks of cytosine and cytosine monohydrate consist of collective vibrations mixed with intermolecular and intramolecular vibrations in mode character analysis, and that the most intense peaks of both samples involve remarkable intermolecular translational vibration. these results indicate that tHz-tDS combined with Dft calculations including mode character analysis can be an effective method for understanding how water molecules contribute to the characteristics of the low-frequency vibrational modes by intermolecular vibrations with hydrogen bonding in biological and biomedical applications.

show abstract

“…Here, we employ QHA approach to interpret our experimental phenomenon. As the London dispersion plays an important role in accurate simulation of geometry and THz spectra of crystals, [11,[37][38][39] we decided to use two most popular dispersion corrections including Grimme's D3 [24] and many-body dispersion [25] in QHA calculations to see whether they differ significantly.…”

Section: Quasi-harmonic Approximation (Qha) Calculationsmentioning

confidence: 99%

“…[5][6][7][8][9] With the assistance of molecular modelling techniques like density functional theory (DFT), the featured peaks in THz spectra can be well reproduced and interpreted. [10][11][12] However, the temperature effects on the THz spectra, which is usually reflected as the frequency shift of absorption peaks, is rarely interpreted by researchers. [13,14] The main reason is that a common solid-state DFT calculation involving geometry optimization and phonon calculation based on the harmonic approximation cannot handle temperature effects.…”

Section: Introductionmentioning

confidence: 99%

Temperature‐Dependent Terahertz Spectra of Isonicotinamide in the Form I Studied Using the Quasi‐Harmonic Approximation

Sun

Lei

et al. 2022

ChemPhysChem

Self Cite

View full text Add to dashboard Cite

Anharmonicity of molecular vibrational motions is closely associated with the thermal property of crystals. However, the origin of anharmonicity is still not fully understood. Lowfrequency vibrations, which are usually defined in the terahertz (THz) range, show excellent sensitivity to anharmonicity. In this work, anharmonicity of isonicotinamide in the form I was investigated by using temperature-dependent terahertz timedomain spectroscopy and the quasi-harmonic approximation (QHA) approach at PBE-D3 and PBE-MBD levels. Both DFT calculations suggest the variation of π-π stacking conformation dominates in the thermal expansion of the unit cell. Frequency shifts of the modes in THz range obtained by QHA approach are found to be qualitatively consistent with experimental observations, demonstrating QHA approach is a useful tool for the interpretation of frequency shifts of modes induced by temperature.

show abstract

The effect of the flexibility of hydrogen bonding network on low-frequency motions of amino acids. Evidence from Terahertz spectroscopy and DFT calculations

Cited by 19 publications

References 34 publications

Vibrational Response of Felodipine in the THz Domain: Optical and Neutron Spectroscopy Versus Plane-Wave DFT Modeling

Vibrational Response of Felodipine in the THz Domain: Optical and Neutron Spectroscopy Versus Plane-Wave DFT Modeling

Transformation of terahertz vibrational modes of cytosine under hydration

Temperature‐Dependent Terahertz Spectra of Isonicotinamide in the Form I Studied Using the Quasi‐Harmonic Approximation

Contact Info

Product

Resources

About