First principles investigation of L-alanine in terahertz region

Zheng, Zhuan‐Ping; Wang, Fan

doi:10.1007/s10867-012-9261-0

Cited by 29 publications

(12 citation statements)

References 33 publications

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“…20 The calculated lattice constants (a, b and c) for CH 3 CHNH 2 COOH, CH 2 FCHNH 2 COOH and CHF 2 CHNH 2 COOH are listed in Table 1. It is clear from the table that our theoretical results are in agreement with the reported experimental results 19,21,3,22 for CH 3 CHNH 2 COOH and CH 2 FCHNH 2 COOH, respectively, while no literature 1650079-3 S. Ahmad et al Table 2. Bond lengths (Å) of L-alanine, monoflouroalanine and difluoroalanine.…”

Section: Structural Propertiessupporting

confidence: 88%

First-principles studies of pure and fluorine substituted alanines

Ahmad

Vaizie

Aliabad

et al. 2016

Int. J. Mod. Phys. B

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This paper communicates the structural, electronic and optical properties of L-alanine, monofluoro and difluoro substituted alanines using density functional calculations. These compounds exist in orthorhombic crystal structure and the calculated structural parameters such as lattice constants, bond angles and bond lengths are in agreement with the experimental results. L-alanine is an indirect band gap insulator, while its fluorine substituted compounds (monofluoroalanine and difluoroalanine) are direct band gap insulators. The substitution causes reduction in the band gap and hence these optically tailored direct wide band gap materials have enhanced optical properties in the ultraviolet (UV) region of electromagnetic spectrum. Therefore, optical properties like dielectric function, refractive index, reflectivity and energy loss function are also investigated. These compounds have almost isotropic nature in the lower frequency range while at higher energies, they have a significant anisotropic nature.

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Section: Structural Propertiessupporting

confidence: 88%

First-principles studies of pure and fluorine substituted alanines

Ahmad

Vaizie

Aliabad

et al. 2016

Int. J. Mod. Phys. B

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“…They concluded that vibrations in low frequencies are mainly from the twisting and rocking motions of intermolecular hydrogen bonds. First principle calculation of the THz spectrum (16.6 -133.3 cm 21 ) of L-alanine crystal by Zheng et al [20] confirmed that the intermolecular vibration in crystal is an important contribution to THz absorption. Through investigations on THz spectra of L-Ala n (n ¼ 1, 2, 3, 5) (0 -60 cm 21 ), Ponseca et al [25] found there is a clear difference in low-frequency dynamics between amino acids and polypeptides.…”

Section: Introductionmentioning

confidence: 94%

Molecular dynamics simulations of conformation and chain length dependent terahertz spectra of alanine polypeptides

Zhang

Wei

Tang

et al. 2015

Molecular Simulation

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Terahertz absorption spectra of alanine polypeptides in water were simulated with classical molecular dynamics at 310 K. Vibrational modes and oscillator strengths were calculated based on a quasi-harmonic approximation. Absorption spectra of Ala n (n ¼ 5, 15, 30) with different chain lengths and Ala 15 in coiled and helical conformations were studied in 10 -40 cm 21 bandwidth. Simulation results indicated both the chain length and the conformation have significant influences on THz spectra of alanine polypeptides. With the increase of chain length, the average THz absorption intensity increases. Compared with the helical Ala 15 polypeptide, the THz spectra of coiled one shows stronger absorption peaks. These results were explained from different numbers of hydrogen bonds formed between polypeptides and the surrounding water molecules.

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“…The structural differences between amino acids depend on the side chain R and its polarity. Most THz biomolecule investigations have been focused on amino acids in the low-frequency spectral interval [118][119][120][121][122][123][124][125][126][127][128][129][130][131], see Table 1. All 20 standard α-amino acids under the same conditions revealed a correlation between molecular structures and spectral peaks between 0.2 and 3.0 THz (6.67-100 cm −1 ) [122].…”

Section: Current Status Of Thz Spectroscopy For Research On Amino Aci...mentioning

confidence: 99%

“…The amino acids were studied in the solid phase, mixing them with a polyethylene powder in various proportions. For example, high proportions of amino acids to polyethylene (1:1 and 2:1) [123,124], as well as low proportions (1:15 and 1:9) [125,126], are used. From these, it emerged that the proportion of amino acids to THz transparent material in the production of the pellet influences the spectrum, especially in the low-frequency region [123,127].…”

Section: Current Status Of Thz Spectroscopy For Research On Amino Aci...mentioning

confidence: 99%

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Terahertz Spectroscopic Analysis in Protein Dynamics: Current Status

et al. 2022

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Proteins play a key role in living organisms. The study of proteins and their dynamics provides information about their functionality, catalysis and potential alterations towards pathological diseases. Several techniques are used for studying protein dynamics, e.g., magnetic resonance, fluorescence imaging techniques, mid-infrared spectroscopy and biochemical assays. Spectroscopic analysis, based on the use of terahertz (THz) radiation with frequencies between 0.1 and 15 THz (3–500 cm−1), was underestimated by the biochemical community. In recent years, however, the potential of THz spectroscopy in the analysis of both simple structures, such as polypeptide molecules, and complex structures, such as protein complexes, has been demonstrated. The THz absorption spectrum provides some information on proteins: for small molecules the THz spectrum is dominated by individual modes related to the presence of hydrogen bonds. For peptides, the spectral information concerns their secondary structure, while for complex proteins such as globular proteins and viral glycoproteins, spectra also provide information on collective modes. In this short review, we discuss the results obtained by THz spectroscopy in the protein dynamics investigations. In particular, we will illustrate advantages and applications of THz spectroscopy, pointing out the complementary information it may provide.

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First principles investigation of L-alanine in terahertz region

Cited by 29 publications

References 33 publications

First-principles studies of pure and fluorine substituted alanines

First-principles studies of pure and fluorine substituted alanines

Molecular dynamics simulations of conformation and chain length dependent terahertz spectra of alanine polypeptides

Terahertz Spectroscopic Analysis in Protein Dynamics: Current Status

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