FTIR spectra and conformations of 2′-deoxyuridine in Kr matrices

Ivanov, А. Yu.; Karachevtsev, V. A.

doi:10.1063/1.2755193

Cited by 22 publications

(10 citation statements)

References 31 publications

(41 reference statements)

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“…It was previously shown 16,17 that low-barrier conformers of nucleosides are fixed in low-temperature matrices more poorly than conformers of small molecules. For example, the syn-conformer of 2 0 -deoxyuridine with C3 0 -endo structure of the sugar ring (the barrier of transition to C2 0 -endo is 1.3 kcal/mol 16 ) is not preserved upon freezing in Ar and Kr matrices even at 6 K. Moreover, transition of the O3 0 H hydroxy group of 2 0 -deoxyuridine molecules through a 1.2 kcal/mol barrier was observed upon deposition into a Kr matrix at 6 K. 17 Approximate estimates of the interconversion time show that in order to fix low-barrier conformers, the cooling time should be comparable to the period of phonon oscillations of the matrix and lowfrequency vibrational modes of molecules. 14 The effect of the matrix on the energy relaxation in impurity molecules was already observed experimentally.…”

Section: Low Temperature Physicsmentioning

confidence: 99%

Nucleoside conformers in low-temperature argon matrices: Fourier transform IR spectroscopy of isolated thymidine and deuterothymidine molecules and quantum-mechanical calculations

Ivanov

Stepanian

Karachevtsev

et al. 2019

Low Temperature Physics

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The conformational equilibrium of thymidine and deuterothymidine molecules in low-temperature Ar matrices has been studied using low-temperature matrix-isolation Fourier IR spectroscopy and quantum-chemical calculations by the DFT/B3LYP and MP2 methods. It has been found that two anti-conformers ta2_0 and ta3_0 with different structures of the sugar ring, C2 0 -endo and C3 0 -endo, predominate in low-temperature matrices. In isolated state, each of these conformers has a few low-barrier satellites that can fully pass into more stable structures when a molecule enters the matrix. The main syn conformer ts2_0 is stabilized by an intramolecular hydrogen bond between the O5 0 H group of the sugar and the C2O group of the base (O5 0 H⋅⋅⋅O2), while C2 0 -endo is the predominant conformation of the deoxyribose ring. The considerably lower population of ts2_0 compared to the anti-conformers ta2_0, ta3_0 can be explained by the smaller population of satellite conformations. It has been shown that the absorption band of νN3D stretching vibration is split by the Fermi resonance.

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Section: Low Temperature Physicsmentioning

confidence: 99%

Nucleoside conformers in low-temperature argon matrices: Fourier transform IR spectroscopy of isolated thymidine and deuterothymidine molecules and quantum-mechanical calculations

Ivanov

Stepanian

Karachevtsev

et al. 2019

Low Temperature Physics

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“…Low-temperature experiment was carried out by using a matrix-isolation FTIR spectroscopy setup described previously. [17][18][19][20] The FTIR spectra of uracil were obtained in the range of 2700-600 cm À1 with an apodized resolution of 1063-777X/2016/42(2)/5/$32.00…”

Section: Experimental and Computational Methodsmentioning

confidence: 99%

Enhancement of infrared absorption of low-temperature uracil thin films by a nanostructured silver surface

Ivanov

Stepanian

Adamowicz

et al. 2016

Low Temperature Physics

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Enhancement of infrared absorption (SEIRA) of adsorbed biological molecules by a nanostructured metal surface is one of the main routes to increasing the sensitivity of modern optical biosensors. The FTIR absorption spectra of thin films of the RNA base uracil deposited on low-temperature substrate (T ¼ 6 K) with nanoscale silver structures were investigated in the spectral range 2700-600 cm-1. It was shown that the intensity of the absorption bands corresponding to CO stretching vibrations (range 1800-1600 cm-1) of uracil (Ur) thin films increases 3-4 fold. For multilayer films, the influence of the nanostructures on the vibrational spectra weakens, and for the film layers more than 15 nm away from the surface, the enhancement is essentially absent. The energies and the vibrational spectra of the complexes of uracil monomers and dimers with 20-atom tetrahedral silver nanoclusters were calculated by the quantum-mechanical method DFT/B3LYP. The most stable complexes have the coordination bond between the top of the silver tetrahedron and the oxygen of the carbonyl group C4O. It was found that the formation of such complexes significantly (3-5 fold) enhances the intensity of the C4O stretching vibration of uracil, while the intensities of the bNH, bCH and ring bending vibrations do not increase significantly.

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“…Измерения инфракрасных Фурье спектров проводились на установке для спектроскопии низкотемпературной матричной изоляции. Особенности этой спектральной установки рассмотрены в ряде наших предыдущих работ [12][13][14][15]. Для создания композитов был использован GO фирмы GRAPHENEA (Spain) в виде водного коллоидного раствора с концентрацией около 2 мг/мл, а также порошок MoS 2 (Sigma-Aldrich Europe), обработанный ультразвуковым диспергатором УЗДН в коллоидном растворе с такой же концентрацией.…”

Section: материалы и методыunclassified

“…Для 5BrU мы рассматривали только дикето-форму, как доминирующую структуру для изолированного состояния молекулы [21]. Расчеты показали, что относительные энергии и заселенность конформационных изомеров 5BrdU достаточно близки к параметрам аналогичных изомеров, рассмотренных нами для 2'-дезокси-уридина и тимидина [13,14,22]. Наиболее характерные представители син-и анти-подмножеств конформационных изомеров 5BrdU показаны на Рис.…”

Section: син-изомер (E=0)unclassified

Spectral and structural features of bio-composite films of graphene oxide and molybdenum disulphide with molecules of 5-bromouracyl and 5-bromo-2’-deoxyuridine

2020

Biophysical Bulletin

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Background: Recently, composite materials based on nanoparticles and biological molecules have been intensively studied due to the unique physicochemical and biophysical properties and prospects of application in various fields of technology, engineering and medicine. Many laboratories conduct experiments with composite materials based on carbon nanoparticles and various 2D nanomaterials in order to create sensitive biosensors based on them, to develop new functional materials for biology and medicine. A wide range of practical applications requires fundamental knowledge about the structure of the created composites, the interaction energy between the components and their spectral characteristics. Objectives: The purpose of the work was to study the structural features of biocomposite films of graphene oxide (GO) and molybdenum disulfide MoS2 with 5-bromouracil (5BrU) and 5-bromo-2'-deoxyuridine (5BrdU) and to obtain information on the interaction between their components based on data from the infrared Fourier spectroscopy and quantum chemical calculations. Materials and methods: For the measurements, a vacuum infrared Fourier spectrometer was used. The composite films were created by the drop casting method based on graphene oxide from GRAPHENEA, an aqueous suspension of MoS2 molybdenum disulfide powder, as well as 5BrU and 5BrdU biomolecules. For the quantum-chemical calculations of model structures the Gaussian 09 and the Firefly 8.0 programs were used. In last one the GAMESS (USA) program code was partially used. Results: The frequencies and intensities of infrared absorption bands of the biocomposite films (5BrU/GO, 5BrU/MoS2, 5BrdU/GO and 5BrdU/MoS2) with different numbers of biomolecules were obtained. The absorption bands of composite films are assigned to the corresponding types of normal vibrations. The interaction energies in model structures are determined. The amorphous (disordered) structure of 5BrU clusters in 5BrU/GO composites at a low concentration of biomolecules has been established. It is shown that the MoS2 composites are more heterogeneous than the GO composites. Conclusions: The absorption band of CO vibrations with a frequency of 1783 cm–1 as well as the bands of the out-of-plane deformation vibrations γNH of 5BrU are sensitive to the structure of 5BrU clusters in composite films. It has been demonstrated that graphene oxide in the composite films affects the conformational equilibrium of 5BrdU. It has been established that structures with stacking between the pyrimidine ring of a nucleoside and the basal plane of graphene oxide are the most energetically favorable.

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FTIR spectra and conformations of 2′-deoxyuridine in Kr matrices

Cited by 22 publications

References 31 publications

Nucleoside conformers in low-temperature argon matrices: Fourier transform IR spectroscopy of isolated thymidine and deuterothymidine molecules and quantum-mechanical calculations

Nucleoside conformers in low-temperature argon matrices: Fourier transform IR spectroscopy of isolated thymidine and deuterothymidine molecules and quantum-mechanical calculations

Enhancement of infrared absorption of low-temperature uracil thin films by a nanostructured silver surface

Spectral and structural features of bio-composite films of graphene oxide and molybdenum disulphide with molecules of 5-bromouracyl and 5-bromo-2’-deoxyuridine

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