Computational investigation of spectroscopic parameters in putative secondary structure elements for polylactic acid and comparison with experiment

Irsai, Izabella; Lupan, Alexandru; Majdik, Cornelia; Silaghi‐Dumitrescu, Radu

doi:10.24193/subbchem.2017.4.42

Cited by 4 publications

(3 citation statements)

References 26 publications

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“…The experimental positions of the absorption peaks are also given in order to verify the reliability of the AIMD-calculated absorption spectra. As shown in these tables, the positions of the predicted absorption peaks are basically consistent with the literature experimental results, [63][64][65][66] but with some exceptions. For instance, the experimental frequencies for PVA show that the absorption peak representing the OH stretching vibration is a broad peak with very strong intensity, whereas the AIMD-calculated result is narrow due to the relatively small computational system used for AIMD calculations.…”

Section: Absorption Spectrumsupporting

confidence: 89%

Combining ab initio and ab initio molecular dynamics simulations to predict the complex refractive indices of organic polymers

Wang

2023

Phys. Chem. Chem. Phys.

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Section: Absorption Spectrumsupporting

confidence: 89%

Combining ab initio and ab initio molecular dynamics simulations to predict the complex refractive indices of organic polymers

Wang

2023

Phys. Chem. Chem. Phys.

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“…Table II presents the vibrational signals of KMB and their assignments based on literature. [23][24][25][26][27][28][29][30] The presence of water in the KMB structure is confirmed by the OH stretching signals observed at 3519 cm À1 and 3455 cm À1 in the IR spectrum and at 3048 cm À1 in the Raman spectrum.…”

Section: Vibrational Analysismentioning

confidence: 99%

Structural, Spectral, and Optical Characterization of Potassium bis(2-methyllactato)borate Hemihydrate Crystal

Gokila¹,

Aarthi²,

Raja³

2020

Journal of Elec Materi

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Potassium bis(2-methyllactato)borate hemihydrate (KMB) was grown by a solvent evaporation technique. Crystal structural analysis revealed that the potassium cation was pseudo-octahedrally coordinated by five O atoms from four bis(2-methyllactato)borate (MB) ligands and half-occupied water. The sharp peaks in the powder x-ray diffraction (PXRD) pattern confirmed the perfect crystalline nature of the KMB. Transparency was observed in the range from 215 nm to 1100 nm, and the bandgap of KMB was determined to be 2.15 eV. The molecular structure of KMB was established by interpreting the functional group vibrations through vibrational spectroscopy. The molecular structure was further confirmed by the nuclear magnetic resonance (NMR) spectral technique. The peak followed by valley nature observed is due to the self-focusing behavior of KMB. The minimum transmission near the focus in the open aperture curve is attributed to the reverse saturation absorption nature of KMB. The third-order susceptibility (v (3) ) of KMB is estimated to be 4.17694 9 10 À5 esu. These results suggest that KMB can be used in optical sensors as well as other photonic and optoelectronic applications.

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“…This was interpreted as either a need to use more appropriate calculation methods, or as evidence that the experimental structure of PLA entails new secondary structure elements, different from those seen in proteins and explored in the computational study. 25 Molecular dynamics simulations were also performed, through which the interfacial interaction of polylactic acid with zirconium and hydroxyapatite surfaces was analyzed. In these interactions, the PLA conformations underwent pronounced changes especially when coupling agents were added to bioceramic systems and polylactic acids.…”

Section: Introductionmentioning

confidence: 99%

A critical review of computational efforts towards identifying secondary structure elements in polylactic acid (PLA)

IRSAI,

PESEK,

SILAGHI-DUMITRESCU

2023

Rev.Roum.Chim.

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Polylactic acid (PLA) may be regarded as an analogue of a poly-alanine oligo/polypeptide, where the amino group has been replaced by a hydroxyl. As a consequence, a series of studies have explored the possibility that PLA can adopt peptide-type secondary structures – i.e., repetitive structural patterns characterized by intramolecular hydrogen bonds between neighboring functional groups. To this end, computational techniques (molecular mechanics, semiempirical, Hartree-Fock, density functional theory DFT) geometry optimizations of isolated oligomers of lactic acid (generally ten-unit oligomers), or oligomers attached to solid surfaces, or dimers have been reported, as well as spectral simulations thereof - looking at relative stabilities of helices (α, π, 310), and β sheets. A significant variation in the predicted structures and spectra was noted, depending on the computational method employed. With the most accurate method available (a DFT functional parametrized especially for describing non-covalent interactions), in isolated PLA models the π helix was found to be the most likely structure, closely followed by the 310 helix, and β sheets being the least stable. We review here these data and add two important elements: (1) first, a comparison with an experimentally-derived model of PLA, proposed by De Santis, and (2) second, a Ramachandran analysis of the Φ and Ψ angles in the optimized geometries. It is shown that (1) the De Santis structure is in fact slightly more stable than the helices, and (2) the optimized geometries in fact stray far from the initial Φ, Ψ values – to the extent that all of the peptide-like secondary structures in fact end up as turns (mostly type III β turns), while the DFT-optimized De Santis structure has no classical correspondent in the Ramachandran series of secondary structures.

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Computational investigation of spectroscopic parameters in putative secondary structure elements for polylactic acid and comparison with experiment

Cited by 4 publications

References 26 publications

Combining ab initio and ab initio molecular dynamics simulations to predict the complex refractive indices of organic polymers

Combining ab initio and ab initio molecular dynamics simulations to predict the complex refractive indices of organic polymers

Structural, Spectral, and Optical Characterization of Potassium bis(2-methyllactato)borate Hemihydrate Crystal

A critical review of computational efforts towards identifying secondary structure elements in polylactic acid (PLA)

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