Библиотека института физики им. Л.В. Киренского СО РАН

Главная

Базы данных

Труды сотрудников ИФ СО РАН - результаты поиска

Вид поиска

Каталог книг и брошюр библиотеки ИФ СО РАН

Каталог журналов библиотеки ИФ СО РАН

Труды сотрудников ИФ СО РАН

Область поиска

в найденном

Формат представления найденных документов:
полный	информационный	краткий

Отсортировать найденные документы по:
автору	заглавию	году издания	типу документа

Поисковый запрос: (<.>K=DFTB<.>)

Общее количество найденных документов : 4
Показаны документы с 1 по 4

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Begunovich L. V., Kovaleva E. A., Korshunov M. M., Shabanov V. F.
Заглавие : Absorption spectra of the purple nonsulfur bacteria light-harvesting complex: A DFT study of the B800 part
Колич.характеристики :7 с
Место публикации : J. Photochem. Photobiol. A: Chem. - 2024. - Vol. 450. - Ст.115454. - ISSN 10106030 (ISSN), DOI 10.1016/j.jphotochem.2023.115454. - ISSN 18732666 (eISSN)
Примечания : Cited References: 42. - This work was supported by the state assignment of the Ministry of Science and Higher Education of the Russian Federation. Authors would like to thank Information Technology Centre, Novosibirsk State University for providing access to their supercomputers. L.V.B. would like to thank Irkutsk Supercomputer Center of SB RAS for providing the access to HPC-cluster «Akademik V.M. Matrosov» (Irkutsk Supercomputer Center of SB RAS, Irkutsk: ISDCT SB RAS; http://hpc.icc.ru, accessed 20.10.2023)
Аннотация: We’ve studied the B800 part of Rhodoblastus acidophilus light-harvesting complex (LH2) by several quantum chemical techniques based on the density functional theory (DFT) and determined the specific method and a minimal reliable model suitable for further studies of the LH2. In addition to bacteriochlorophyll a molecules, the minimal model includes two α and one β chain amino acids. Within the model, we are able to reproduce the contribution of the B800 ring of nine bacteriochlorophyll a molecules to the near infrared Qy absorption band. We also discuss the use of hybrid DFT calculations for precise energy and optical estimations and DFT-based tight binding (DFTB) method for the large-scale calculations. Crucial importance of Hartree-Fock exchange interaction for the correct description of B800 peak position was shown.
Смотреть статью,
Scopus,
WOS
Найти похожие

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Shchugoreva I. A., Artyushenko P. V., Tomilin F. N., Morozov D. I., Mironov V. A., Moryachkov R. V., Kichkailo A. S.
Заглавие : Applying joint theoretical experimental research to aptamer modeling
Место публикации : Sib. Med. Rev. - 2021. - Vol. 2021, Is. 2. - P.105-106. - ISSN 18199496 (ISSN), DOI 10.20333/2500136-2021-2-105-106; Сиб. мед. обозрение
Примечания : Cited References: 4
Аннотация: The aim of the research. In this work we studied the structure of LC-18 DNA aptamer, which exhibits specific binding to lung adenocarcinoma cells. Obtain-ing the 3D structure of the aptamer is necessary for understanding the mechanism of binding of the aptamer to the target. Therefore, the aim of the research was modeling of the LC-18 aptamer spatial structure using combination of theoretical methods: DNA folding tools, quantum-chemical calculations and molecular dynamic simulations. Material and methods. The secondary structure of the LC-18 aptamer was predicted by using OligoAnalyzer and MFold online software under the conditions typical small-angle X-ray scattering (SAXS) experiment. The molecular modeling of the aptamer was carried out using the Avogadro program. For prediction of the structure two computational methods were used: quantum-mechanical method with third-order density-functional tight-binding (DFTB3) and molecular dynamics (MD) with force fields. Results. In this paper it was shown that molecular simulations can predict structures from the SAXS experiments. OligoAnalyzer and MFold web servers have been used to generate a set of several likely models. However, more accurate calculations have showed that these models do not predict the relative importance of isomers. Meanwhile, application of quantum-chemical and molecular dynamics calculations have showed reliable molecular structures which have a small deviations from the experimental SAXS curves. Conclusion. This study demonstrates the approach for modeling 3D structures of DNA-aptamers in solution using both experimental and theoretical meth-ods. It could be very helpful in designing more efficient aptamers based on results obtained from molecular simulations.
Смотреть статью,
РИНЦ,
Scopus,
Читать в сети ИФ
Найти похожие

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Kudryavtsev, Alexander N., Krasitskaya, Vasilisa V., Efremov, Maxim K., Zangeeva, Sayana V., Rogova A. V., Tomilin F. N., Frank, Ludmila A.
Заглавие : Ca2+-triggered coelenterazine-binding protein Renilla: Expected and unexpected features
Место публикации : Int. J. Mol. Sci. - 2023. - Vol. 24, Is. 3. - Ст.2144. - ISSN 16616596 (ISSN), DOI 10.3390/ijms24032144. - ISSN 14220067 (eISSN)
Примечания : Cited References: 24. - This research was supported by the state budget allocated to the fundamental research at the Russian Academy of Sciences, project No. 0287-2022-0002 and the Interagency Supercomputer Center of the Russian Academy of Sciences, MVS-100K and MVS-10P
Аннотация: Ca2+-triggered coelenterazine-binding protein (CBP) is a natural form of the luciferase substrate involved in the Renilla bioluminescence reaction. It is a stable complex of coelenterazine and apoprotein that, unlike coelenterazine, is soluble and stable in an aquatic environment and yields a significantly higher bioluminescent signal. This makes CBP a convenient substrate for luciferase-based in vitro assay. In search of a similar substrate form for the luciferase NanoLuc, a furimazine-apoCBP complex was prepared and verified against furimazine, coelenterazine, and CBP. Furimazine-apoCBP is relatively stable in solution and in a frozen or lyophilized state, but as distinct from CBP, its bioluminescence reaction with NanoLuc is independent of Ca2+. NanoLuc turned out to utilize all the four substrates under consideration. The pairs of CBP-NanoLuc and coelenterazine-NanoLuc generate bioluminescence with close efficiency. As for furimazine-apoCBP-NanoLuc pair, the efficiency with which it generates bioluminescence is almost twice lower than that of the furimazine-NanoLuc. The integral signal of the CBP-NanoLuc pair is only 22% lower than that of furimazine-NanoLuc. Thus, along with furimazine as the most effective NanoLuc substrate, CBP can also be recommended as a substrate for in vitro analytical application in view of its water solubility, stability, and Ca2+-triggering “character”.
Смотреть статью,
Scopus,
WOS,
Читать в сети ИФ
Найти похожие

Вид документа : Статья из журнала
Шифр издания :
Автор(ы) : Tomilin F. N., Artyushenko P. V., Shchugoreva I. A., Rogova A. V., Vnukova N. G., Churilov G. N., Shestakov N. P., Tchaikovskaya O. N., Ovchinnikov S. G., Avramov P. V.
Заглавие : Structure and vibrational spectroscopy of C82 fullerenol valent isomers: An experimental and theoretical joint study
Место публикации : Molecules. - 2023. - Vol. 28, Is. 4. - Ст.1569. - ISSN 14203049 (eISSN), DOI 10.3390/molecules28041569
Примечания : Cited References: 57. - Synthesis and spectroscopic study of the Gd@C82OxHy complexes were supported by the Ministry of Science and Higher Education of the Russian Federation under project FWES-2022-0005. Molecular design of the fullerene derivatives was supported by the National Research Foundation of the Republic of Korea, grant NRF 2021R1A2C1010455. DFTB3 electronic structure calculations were supported by Project FSWM-2020-0033 of the Russian Ministry of Science and Education
Аннотация: Gd@C82OxHy endohedral complexes for advanced biomedical applications (computer tomography, cancer treatment, etc.) were synthesized using high-frequency arc plasma discharge through a mixture of graphite and Gd2O3 oxide. The Gd@C82 endohedral complex was isolated by high-efficiency liquid chromatography and consequently oxidized with the formation of a family of Gd endohedral fullerenols with gross formula Gd@C82O8(OH)20. Fourier-transformed infrared (FTIR) spectroscopy was used to study the structure and spectroscopic properties of the complexes in combination with the DFTB3 electronic structure calculations and infrared spectra simulations. It was shown that the main IR spectral features are formed by a fullerenole C82 cage that allows one to consider the force constants at the DFTB3 level of theory without consideration of gadolinium endohedral ions inside the carbon cage. Based on the comparison of experimental FTIR and theoretical DFTB3 IR spectra, it was found that oxidation of the C82 cage causes the formation of Gd@C82O28H20, with a breakdown of the integrity of the parent C82 cage with the formation of pores between neighboring carbonyl and carboxyl groups. The Gd@C82O6(OOH)2(OH)18 endohedral complex with epoxy, carbonyl and carboxyl groups was considered the most reliable fullerenole structural model.
Смотреть статью,
WOS,
Читать в сети ИФ
Найти похожие