Low-frequency Raman spectra of polycrystalline ribonucleosides

Hovorun, Dmytro М.; Mishchuk, Ya. R.; Yurenko, Ye. P.

doi:10.7124/bc.000601

Cited by 5 publications

(3 citation statements)

References 14 publications

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“…For the identification and characterization of the synthesized La(2b') 3 coordination complex, a detailed analysis of the calculated and experimental spectra was carried out. Low-lying molecular vibrations have been studied by different authors [42][43][44][45], and their presence indicates a high flexibility in the molecular structure that may be caused by various factors. Moreover, in our La(2b') 3 complex, the normal vibrational modes that include the lanthanide ion mainly appear below 200 cm −1 .…”

Section: Vibrational Analysismentioning

confidence: 99%

Structural Study of a La(III) Complex of a 1,2,3-Triazole Ligand with Antioxidant Activity

Alcolea Palafox,

Belskaya,

Todorov

et al. 2023

Antioxidants

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The 1,2,3-triazole derivative 2-(4-chlorophenyl)-5-(pyrrolidin-1-yl)-2H-1,2,3-triazole-4-carboxylic acid with potential anticancer activity was used as a ligand in complex formation with the lanthanum(III) ion. The molecular structure and vibrational spectra of the complex were optimized at three DFT levels, and the scaled IR and Raman spectra were compared to the experimental ones. Several scaling procedures were used. Through a detailed analysis, the structure predicted for the newly synthetized La(III) complex was confirmed by the good accordance of the calculated/experimental IR and Raman spectra. The best DFT method appeared to be M06-2X with the Lanl2mb basis set, followed closely by Lanl2dz. The effect of the lanthanide atom on the molecular structure and atomic charge distribution of the triazole ring was evaluated. The potential free radical scavenging activity of both the ligand and the complex was investigated in several radical-generating model systems. The potential mechanisms of antioxidant action (hydrogen atom transfer (HAT) and single-electron transfer (SET)) were elucidated.

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Section: Vibrational Analysismentioning

confidence: 99%

Structural Study of a La(III) Complex of a 1,2,3-Triazole Ligand with Antioxidant Activity

Alcolea Palafox,

Belskaya,

Todorov

et al. 2023

Antioxidants

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“…Although Equation (1) appears to be a useful tool that bridges electron topological and energetic characteristics of hydrogen bonds, it is confined only to hydrogen‐bonding contacts in which the oxygen atom acts as an acceptor. Moreover, there is a substantial piece of evidence that, with the commonly used coefficient c =1/2, Equation (1) tends to overestimate the energy of weak hydrogen bonds; this is mainly because it has been parameterized by using data for substances in the crystalline state, in which hydrogen bonds are effectively strengthened . Therefore, the coefficient in Equation (1) should be reparameterized for each hydrogen‐bond type by taking into account the class of molecular system and environment.…”

Section: Computational Detailsmentioning

confidence: 99%

Weak Supramolecular Interactions Governing Parallel and Antiparallel DNA Quadruplexes: Insights from Large‐Scale Quantum Mechanics Analysis of Experimentally Derived Models

Yurenko

Novotný

Marek

2017

Chemistry A European J

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The topology and energetics of guanine (G) quadruplexes is governed by supramolecular interactions within their strands. In this work, an extensive quantum mechanical (QM) study has been performed to analyze supramolecular interactions that shape the stems of (4+0) parallel (P) and (2+2) antiparallel (AP) quadruplex systems. The large-scale (≈400 atoms) models of P and AP were constructed from high-quality experimental structures. The results provide evidence that each of the P and AP structures is shaped by a distinct network of supramolecular interactions. Analysis of electron topological characteristics of hydrogen bonds in P and AP systems indicates that the P model benefits from stronger intratetrad hydrogen bonding. For intertetrad stacking interactions, both noncovalent interaction plot and energy decomposition analysis approaches suggest that the stem of the P quadruplex benefits more from stacking than that of the AP stem; the difference in energetic stabilization for the two topologies is about 10 %. Stronger hydrogen-bonding and stacking interactions in the stem of the P quadruplex, relative to those in the AP system, can be an important indicator to explain the experimental observations that guanine-rich oligonucleotides tend to form all-parallel stems with an all-anti orientation of nucleobases. However, in addition to intrinsic stabilization, partial desolvation effects, which affect the energetics and dynamics of the G-quadruplex folding process, call for further investigations.

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“…Low-lying molecular vibrations have been studied by several authors [63][64][65], and their presence indicates a high flexibility in the molecular structure, which may be caused by various factors. Twenty-nine frequencies below 200 cm 1 were found in the complex with Cu, corroborating its high flexibility, while in the complex with Zn, 28 were found and in the complex with Ni, 26 were found.…”

Section: Metal Complexes (With Az In Pmma Films)mentioning

confidence: 99%

Theoretical Interpretation of Polarized Light-Induced Supramolecular Orientation on the Basis of Normal Mode Analysis of Azobenzene as Hybrid Materials in PMMA with Chiral Schiff Base Ni(II), Cu(II), and Zn(II) Complexes

Ito

Akitsu

Palafox

2016

J. Appl. Sol. Chem. Model.

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We have prepared hybrid materials of azobenzene and chiral Schiff base Ni(II), Cu(II), and Zn(II) complexes and investigated their linearly or circularly polarized UV (ultraviolet) light-induced supramolecular orientation with polarized electronic and IR spectra or CD (circular dichroism) spectra. The experimental FT-IR (Fourier transfer-infrared) spectra of azobenzene molecules were recorded at room temperature, and the results were compared with quantum chemical theoretical values using B3LYP, M052X, and M062X DFT (density functional theory) methods. The interaction of azobenzene with PMMA was simulated. Molecular geometry, vibrational wavenumbers, and thermodynamic parameters were calculated in all these systems. With the help of specific scaling procedures for the computed wavenumbers, the experimentally observed FT-IR bands were analyzed and assigned to different normal modes of the molecule. Most modes had wavenumbers in the expected range, and the error obtained was in general very low. Several general conclusions were deduced.

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Low-frequency Raman spectra of polycrystalline ribonucleosides

Cited by 5 publications

References 14 publications

Structural Study of a La(III) Complex of a 1,2,3-Triazole Ligand with Antioxidant Activity

Structural Study of a La(III) Complex of a 1,2,3-Triazole Ligand with Antioxidant Activity

Weak Supramolecular Interactions Governing Parallel and Antiparallel DNA Quadruplexes: Insights from Large‐Scale Quantum Mechanics Analysis of Experimentally Derived Models

Theoretical Interpretation of Polarized Light-Induced Supramolecular Orientation on the Basis of Normal Mode Analysis of Azobenzene as Hybrid Materials in PMMA with Chiral Schiff Base Ni(II), Cu(II), and Zn(II) Complexes

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