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7I. ХИМИЯ И ХИМИЧЕСКАЯ ТЕХНОЛОГИЯ
Неорганическая и физическая химия
УДК 544.1, 544.02
Rashad Abbas12, Nikolay A. Charykov13, Svetlana G. Izotova1, Viktor A.Keskinov4*, Dmitrii G. Letenko5
DENSITY FUNCTIONAL THEORY CALCULATION FOR FULLERENE-LYSINE SYSTEM
1St. Petersburg State Institute of Technology, St. Petersburg, Russian Federation
2Al-Baath University, Homs, Syrian Arab Republic
3St. Petersburg State Electrotechnical University "LETI", St.
Petersburg, Russian Federation
4Center "Veritas", D. Serikbayev East Kazakhstan State Technical University, Ust-Kamennogorsk, Kazakhstan 5St. Petersburg State University of Architecture and Civil Engineering, St. Petersburg, Russian Federation [email protected]
The C6e-lysine adduct was synthesized using C0 and lysine as starting materials and characterized by elemental analysis, HPLC, electron spectroscopy, DTG-TG and FT-IR. Elemental analysis revealed the calculated formula of the crystalline hydrate of the bis-adduct C and lysine: CJC6H1NP2)2'5HQ. According to the HPLC chromatogram, the final product comprises lysine and has a purity of 98 rel. masses. %. The electronic spectrum of an aqueous solution of the adduct shows that the resultant chemical is free of starting material impurities. DFT studies of the adduct molecule (fullerene-lysine) were carried out with extensive and precise studies of detailed vibrational and spectroscopic studies and compared with experimental data. Quantum-chemical calculations of geometric optimization and vibra-tional spectra, which were performed in the Gaussian 09 software package, indicate a possible preferable coordination through the NH group. Good agreement between the experimental and2 calculated data in the range of stretching vibrations of OH groups (3460 and 3446 cm-1) and bending vibrations of COH (1446 and 1441 cm-1) allows us to make an assumption in favor of e-NH2 coordination.
Key words: C60-lysine adduct; quantum-chemical modeling, density functional theory (DFT); type of coordination, Gaussian 09 software
DOI 10.36807/1998-9849-2024-71-97-3-8
Introduction
Water-soluble derivatives of light fullerenes are a very interesting class of compounds due to their interesting chemical, physical and biological properties and, therefore, promising possibilities of application in various fields of science and technology, in particular in mechanical engineering, construction, medicine, pharmacology and other fields [1-6]. Among them are fullerenes associated with amino acids and peptides, which have been the subject of many scientific studies, since they represent an important set of compounds
Аббас Р.1'2, Чарыков Н.А.13, Изотова С.Г.1, Кескинов В.А.4,
Летенко Д.Г.5
РАСЧЕТЫ НА БАЗЕ ТЕОРИИ ФУНКЦИОНАЛ ПЛОТНОСТИ В ФУЛЛЕРЕН-ЛИЗИНОВОЙ СИСТЕМЕ
1Санкт-Петербургский государственный технологический институт (технический университет), Санкт-Петербург, Российская Федерация
2Университет Аль-Баас, г. Хомс, Сирийская Арабская республика
3Санкт-Петербургский государственный электротехнический университет "ЛЭТИ", Санкт-Петербург, Российская Федерация 4Центр "Veritas", Восточно-Казахстанский государственный технический университет им.Д.Серикбаева, г. Усть-Каменногорск, Республика Казахстан
5Санкт-Петербургский государственный архитектурно-строительный университет, Санкт-Петербург, Российская Федерация [email protected]
Аддукт Сы-лизина был синтезирован с использованием Сы и лизина в качестве исходных материалов и охарактеризован с помощью элементного анализа, ВЭЖХ, электронной спектроскопии, DTG-TG и FT-IR. Элементный анализ показал расчетную формулу кристаллогидрата бис-аддукта Сы и лизина: C6g(C/H1N2O2)2'5H2O. Согласно хроматограмме ВЭЖХ, конечный продукт содержит лизин и имеет чистоту 98 относительных мас. %. Электронный спектр водного раствора аддукта показывает, что полученный химический продукт не содержит примесей исходного материала. Были проведены DFT-исследования молекулы аддукта (фуллерен-лизина) с использованием обширных и точных исследований, детальных вибрационных и спектроскопических исследований и сравнений с экспериментальными данными. Квантово-химические расчеты геометрической оптимизации и колебательных спектров, которые были выполнены в программном пакете Gaussian Ы9, указывают на возможную предпочтительную координацию через группу £-NH2. Наблюдается хорошее соответствие между экспериментальными и расчетными данными.
Ключевые слова: аддукт С60-лизина; квантово-хими-ческое моделирование; теория функционала плотности (DFT); тип координации; программное обеспечение Gaussian 09
Дата поступления - 28 июня 2Ы24 года Дата принятия - 17 июля 2Ы24 года
that have biological activity and play a special role in the development of drugs, including anti-cancer drugs, and other medical applications [7-10].
As examples of adducts of light fullerene C60 with amino acids, there is information about adducts of C60 with lysine [7-10], threonine [7, 10], hydroxyproline [7], argi-nine [8, 9], glycine [9], asparagine [9], etc. One of the most important adducts of C60 with amino acids are the adducts of C60-lysine, which, according to the literature, were previ-
ously synthesized using various synthesis methods [11-14]. However, the previously synthesized C60-lysine adducts have different structures, and therefore different types of coordination of the lysine molecule(s) to the fullerene core, which will definitely affect the functional properties and expected applications of these adducts. Therefore, it is necessary to determine the nature of the bond between the C60 and lysine molecules, which is not only of theoretical interest, but also leads to interesting conclusions about the nature of biological and molecular-specific interactions. One of the ways to solve this problem is to use quantum chemical modeling [15-18], including quantum-chemical calculation of the IR spectra of the proposed adduct structures with their subsequent comparison with the IR spectrum of the synthesized adduct.
In this work, an attempt is carried out to solve this problem by quantum-chemical modeling of vibrational spectra and comparison of the latter with experimental ones using the example of the adduct of fullerene C60 and the essential amino acid lysine.
Materials and Methods. Experimental
Synthesis. The synthesis of the adduct of fullerene C60 and lysine was carried out according to the following procedure. Lysine (C6HN2O?-HCl) (3.9 g) and sodium hydroxide (15.76 g) were dissolved in 54 ml of water, after which 267 ml of ethanol were added to the resulting solution. Next, a saturated solution of fullerene C (7.62 g) in o-xylene (130 ml) was prepared. Then the resulting solutions were combined and stirred for 7 days at room temperature (the progress of the reaction was monitored using TLC monitoring). Further, the "xylene" phase was separated from the "aqueous-alcoholic" phase. To isolate the adduct of fullerene C60 with lysine, methanol was added to the "water-alcohol phase", the re-crystallization procedure was repeated 3 times. The resulting compound was dried at 60°C for 8 hours.
Characterization. The obtained compound was identified by a complex of physicochemical methods, including elemental analysis, high performance liquid chromatog-raphy (HPLC), electron spectroscopy, simultaneous thermal analysis (DTA-TG), and Fourier-transform infrared spectroscopy (FT-IR).
Elemental analysis of the synthesis product was carried out on a «CHN-628C (LECO)» analyzer. High performance liquid chromatography (HPLC) was performed on a «Hitachi Chromaster» chromatograph. Eluent acetonitrile was o-xylene, chromatographic column was C8-18, spec-trophotometric detection at a wavelength of 330 nm. The electronic spectrum of an aqueous solution of the adduct with respect to pure water in the visible and near ultraviolet regions of the spectrum was obtained using a «SPECORD M-32» spectrophotometer in "KV-1" quartz cells 1 cm wide in the wavelength range 200-900 nm. A saturated solution of the fullerene adduct in water was obtained by isothermal saturation in ampoules, and the solubility was studied at a temperature of 25 °C. The saturation conditions were as follows: saturation time t = 6 h, saturation temperature was maintained with an accuracy of 0.05 °C, saturation was carried out under the conditions of a shaker-thermostat, analysis for the adduct content in the solution was carried out using electronic spectra at a wavelength of 330 nm. Simultaneous thermal analysis was carried out on a synchronous thermal analyzer «NETZSCH STA 449 F3». Heating rate was 10 K/min, open volume was atmosphere-air, temperature range was 40-1100 °C. IR spectra were obtained using a «Shimadzu IRTracer-100 FTIR spectrophotometer» in the range of 4004000 cm-1 in KBr tablets.
Quantum-chemical modeling. Quantum-chemical calculations of geometric optimization and vibrational spectra were performed in the Gaussian 09 software package [19] using Density Functional Theory (DFT) method using the B3LYP hybrid (exchange-correlation) functional. The Pople basis sets were used as the basis sets: 6-31G(d, p), since it
was consistently shown that it is able to reproduce well the experimental structures of organic molecules [20, 21]. The formation of the input and analysis of the output files was carried out using the GaussView 5.0 visualization program [22]. The values of the wavenumbers of vibrations were corrected using the appropriate correlation coefficients [23].
Results and Discussion
Elemental analysis showed the presence of nitrogen in the resulting product. The ratio of carbon, nitrogen and hydrogen practically corresponds to the calculated formula of the crystalline hydrate of the bis-adduct C60 and lysine: Ccn(C,H,.N,O,)-5H,O. The obtained data are shown in Table
6UV 6 14 2 2y2 2 1.
Table 1. Elemental composition of the obtained adduct
Theoretical content (wt.%)
Experimental content (wt.%)
N C H O N C H O
5.0 78 3.8 13 5.1 78 3.5 13
Figure 1 shows an example of an HPLC chromatogram of the obtained adduct of light fullerene C60 and lysine. This chromatogram shows that the resulting product contains lysine and corresponds to a purity of 98 rel. masses. %.
Figure 1. Chromatogram of an aqueous adduct of light fullerene C0 and lysine
The electronic spectrum of an aqueous solution of the adduct relative to pure water in the visible and near ultraviolet regions of the spectrum is shown in Figure 2. It should be noted that the electronic spectrum does not contain absorption bands of the individual fullerene C60, which, in turn, is evidence that the resulting compound doe6s0 not contain any impurities of the starting material.
Figure 3 shows the dependence of optical density on concentration at a wavelength of 330 nm. It can be seen that the Bouguer-Lambert-Beer law is fulfilled in the entire concentration region. The concentration was calculated using simple formula:
C(g/dm3) = 0.0544D330 (l = 1 cm)
(1).
According to Figure 4, TG-curve or dependence (m/m0)-100%, where m and m0 are current and initial sample weights for the amino acid lysine (C6H14N2O2), respectively, shows that it is thermally unstable under experimental conditions: lysine begins to decompose at a temperature of about 260 °C and decomposes completely at about 500 °C, and at 350 °C (m/m.y100% ~ 20. Figure 4 also shows the DTG curve
of the bis-adduct: crystalline hydrate C(C6HN2O2)2
5H2O.
It
can be seen that the crystalline hydrate first loses crystallization water, then at temperatures of about 170-220 °C oxidative thermal destruction of 6 the amino acid residue of the
Figure 2. Electronic spectrum of an aqueous solution of the adduct of fullerene Cm with lysine relative to distilled water (concentration of the adduct C = 0.0299 g/dm3)
tum-chemical data, we first modeled the adduct structures consisting of one fullerene molecule and one lysine molecule, after which we added another lysine molecule. We assumed that during the formation of a bond in the adduct, the hydrogen cleaved from the functional group is attached to the neighboring carbon atom of the fullerene core. Our simulated geometrically optimized adduct structures with binding op-
tions through a-NH2, Figure 5.
£-NH2, or COOH groups are shown in
Figure 3. Feasibility of the Bouguer-Lambert-Beer law in an aqueous solution of the adduct of fullerene C0 with lysine C60(C6H14N,p2)2 at a wavelength of A = 330! nm
fullerene core begins, accompanied by successive processes: internal dehydration (- H2O), denitrogenation (- N2), decar-boxylation (- CO2 and - CO). These stage processes are completed at temperatures of about 720-830 °C, i.e. fullerene core C60 substantially stabilizes amino acid residues. Finally, at temperatures of about 750-850 °C, oxidative destruction of the fullerene core begins.
Figure 5. Geometrically optimized structures of an adduct with one lysine molecule depending on the coordination option: via a-NH2, £-NH, COOH - groups
Among the main differences in the IR spectra of adducts with the composition of "fullerene-one lysine molecule" are shown in Figure 6, it should be noted that there is no stretching vibration of the hydroxyl group when coordinated through the COOH group and its presence when coordinated through the amino group is about 3750 cm-1. The expect-edly different number of vibrations of the amine groups is observed: two asymmetric stretching and two symmetric in the case of COOH-bonding and three vibrations in coordination with fullerene through the amine group: symmetric NH2, asymmetric NH2, and NH stretching vibrations. The intensity of these vibrations is insignificant, and therefore the vibrations cannot be used to confirm the type of coordination in the analysis of the experimental IR spectrum. Some hope for determining the nature of the binding can be given by an analysis of the deformation vibrations of amine groups at about 850-900 cm-1 in view of their greater intensity in the experimental spectrum and the lesser effect on them, apparently, of various types of interactions, which are possible, most likely, as between adduct molecules and water molecules in real systems.
Using quantum-chemical calculations, we were able to determine the position of stretching vibrations responsible for the formation of bonds in the molecules of the adduct
Figure 4. An example of a DTG curve for C6f^(CiHl:N2O:^)2^5H2O
Computational results
Despite the results of elemental analysis that in the adduct structure there are two lysine molecules per fullerene molecule, in order to avoid difficulties in interpreting quan-
Figure 6. Theoretically calculated and experimental IR spectra of adducts with one lysine molecule depending on the coordination option: through a-NH, £-NH2 ant
COOH - groups 2 2
with the composition of "fullerene-one lysine molecule": 1129 cm-1 (C-N) when coordinated through a-NH2, 1122 cm-1 (C-N) - through £-NH2 and 972 cm-1 (C-O) - through COOH groups.
When constructing models for the adduct of the composition of "fullerene-two lysine molecules", we proceeded from the fact that, most likely, the most probable is the attachment of two lysine molecules from opposite sides of the fullerene core at an angle of 180° between them. Variants of bond formation between fullerene and lysine molecules were suggested through either a-NH2, £-NH2, or COOH groups in the cis and trans positions. The hydrogen cleaved from the amino acid during the formation of a bond with fullerene was attached to the neighboring atom of the fullerene core either between the pentagon (5) and hexagon (6) (5-6, blue balls), or between two hexagons (6-6, green ball). Variants of cis-, trans-attachment of lysine to fullerene are shown in Figure 7a, and variants of the arrangement of hydrogen during bond formation are shown in Figure 7b.
ed among other vibrations of lysine and the fullerene core and, most likely, cannot be easily identified in the experimental spectrum. The wavenumbers of the wagging vibration £, £'-NH2 860 cm-1) are close to the experimental values (~ 847 cm-1). The bending vibration of the COH group (~ 1291 cm-1), according to calculations, is strongly shifted relative to the experimentally observed broad peak at about 1446 cm-1.
Figure 7. Variants of cis-, trans-addition of two lysine molecules (Lys, Lys') to fullerene (a), Variants of the arrangement of hydrogen during the formation of a bond with fullerene (b)
When coordinating through the a-NH2 group in the vibrational spectra, we assigned the vibrations of the main characteristic groups, and they are presented in Table 2.
Symmetric and asymmetric stretching vibrations of the £-NH2-group in the range of 3460-3570 cm-1. According to the calculation results, the stretching vibration of the OH--group is about 3795 cm-1, while in the experimental spectrum there is a broad intense peak, which is most likely the result of the superposition of symmetric and asymmetric stretching vibrations of water and the stretching vibration of OH--group, is at lower values of wave numbers 3460 cm-1). In the region of wavenumbers below 2000 cm-1, the calculated IR spectrum shows an intense stretching vibration of C=O at about 1860 cm-1 or its splitting with decreasing intensity is characteristic of cis-coordination. The stretching vibration Cf-N (~ 1130 cm-1) has an insignificant intensity and is locat-
Figure 8. Theoretical and experimental IR spectra of fullerene adducts with two lysine molecules during the formation of a bond through the a-NH2 group
When fullerene-lysine is coordinated through the COOH group, the calculated spectra lack OH stretching vibrations and bending vibrations of COH groups, the absence of these vibrations in the theoretical spectra and, conversely, the presence of the latter in the experimental one excludes the possibility of such a variant of coordination. The stretching vibration Cf-H was found at about 3050 cm-1 and its intensity is low. In the range 750-1300 cm-1, there is a series of high-intensity peaks of characteristic vibrations {v(CLys-O), S(Cf-H), t(CH2), w(NH2)>, which are absent, however, in the experimental spectrum. A clear stretching vibration of C=O (~ 1825 cm-1) and a wagging vibration of a, a'-NH2 and £, £'-NH2-groups (~ 860 cm-1) can be distinguished. The considered type of coordination does not appreciably affect the position of the wagging vibrations of NH2 groups.
The greatest agreement with the2 experimental spec-
Table 2. Energies and assignment of the main bands in the theoretical IR spectra of the proposed C6e-2Lys adduct structures in addition to the experimental IR spectrum of the synthesized adduct
Type of Energy (kJ/ Assignment
coordination mol) ш(1\1Н2) v(Cf-O) v(Cf-N) 5(COH) vfOH) v(Cf-H)
cis, 5-6 -8612140 869, 847 m - 1133, 1116 w 1442, 1441 s 3446, 3444 br s 3055, 3053 vw
trans, 5-6 -8612144 849, 847 m - 1129, 1120 w 1441, 1440 s 3449, 3446 br s 3033, 3029 vw
w cis, 6-6 -8612307 850, 849 m - 1135, 1134 w 1442, 1441 s 3446, 3445 br s 3061, 3059 vw
trans, 6-6 -8612297 849, 848 m - 1138, 1123 w 1442, 1441 s 3446, 3445 br s 3033, 3032 vw
cis, 5-6 -8612216 888, 870 m - 1130, 1122w 1291, 1288 s 3793, 3789 br s 3036, 3025 vw
trans, 5-6 -8612216 858, 849 m - 1124, 1116 w 1292, 1291 s 3796, 3795 br s 3036, 3026 vw
à cis, 6-6 -8612346 869, 859 m - 1127, 1122w 1292, 1291 s 3788, 3741 br s 3062, 3061 vw
trans, 6-6 -8612361 859, 851 m - 1128, 1123 w 1291, 1290 s 3796, 3795 br s 3050, 3039 vw
cis, 5-6 -8612153 858, 857 m 983, 978 w - - - 3066, 3038 vw
X о trans, 5-6 -8612155 863, 859 m 985, 984 w - - - 3064, 3063 vw
о и cis, 6-6 -8612308 861, 860 m 989, 988 w - - - 3069, 3068 vw
trans, 6-6 -8612291 862, 857 m 995, 975 w - - - 3051, 3050 vw
Experimental - 847 - - 1446 3460 -
Cf—fullerene C60 carbon which is bound to lysine, s—strong, m—medium, w—weak, br—broad, v—very
Figure 9. Theoretical and experimental IR spectra of fullerene adducts with two lysine molecules during the formation of a bond through the £-NH-group
Figure 10. Theoretical and experimental IR spectra of fullerene adducts with two lysine molecules during the formation of a bond through the OH-group
tra is shown by the theoretically calculated spectra for the variant of fullerene-lysine coordination through the £-NH2-group (Table 2). The positions of closely spaced peaks of very low intensity, namely: stretching vibrations of £-NH (~ 3506 cm-1) and stretching symmetric and asymmetric vibrations of the a-NH2-group (~ 3601 cm-1) and a higher intensity of stretching vibrations of OH- (~ 3447 cm-1) are consistent with the experimental peak (~ 3460 cm-1). It should be noted that the calculated and experimental wavenumbers are close at 1441 cm-1 and 1446 cm-1, respectively, which we assigned to the bending vibration of the COH group. Some inconsistency in the position of the C=O stretching vibration between experiment and calculation is most likely caused by the presence of possible associative interparticle interactions between terminal COOH groups with other adduct molecules. In the region of wagging vibrations of a, a'-NH2-groups, the values are close to wagging vibrations of £, £'-NH2 at a-coordination. It should be noted that two vibrations are characterized by the highest intensity: the simultaneous wagging vibration of both a-NH2 groups at 849 cm-1 and the joint vibration of the a-NH2 group and the twisting vibration of the COH group at 867 cm-1. Stretching vibrations Cf-N in the region of 11231138 cm-1 are characterized by low intensity. The form of the spectrum is practically unaffected by the variant of addition of hydrogen split off from lysine to the neighboring carbon atom of the fullerene core, but the trans--coordination is slightly more energetically preferable. From a comparison of the experimental and calculated results of the vibrational spectra, despite the close energies, one can conclude in favor of the formation of a fullerene-lysine bond through the £-NH2 group
and completely exclude the variant through the COOH group.
It was found that varying the location of hydrogen cleaved from the coordinating lysine group on the core surface practically does not affect the energy characteristics of the simulated adduct structures and their vibrational spectra, indicating only a slightly higher preference for lysine addition at the interface between two hexagons.
Conclusions
In this work, the synthesis and analysis of the fuller-ene-lysine adduct is carried out using experimental research methods. The results are supplemented by quantum-chemical modeling of adducts of different compositions and types of binding. The calculated vibrational spectra are compared with experimental data in order to clarify the nature of the bond formation between fullerene and lysine. The best agreement of the vibrational spectra was found for the fullerene-two lysine model, which agrees with the experimental data. The most probable type of fullerene-lysine binding corresponds to coordination via £-NH2. The positions of the characteristic vibrations responsible for the fullerene-lysine bond were determined.
Заключение
В данной работе проведен синтез и экспериментальный анализ аддукта фуллерен-лизин. Результаты дополнены квантово-химическим моделированием аддуктов различного состава и типов связывания. Рассчитанные колебательные спектры сравниваются с экспериментальными данными, чтобы прояснить природу образования связи между фуллереном и лизином. Хорошее соответствие колебательных спектров было обнаружено для модели "фуллерен-две молекулы лизина", которая наилучшим способом согласуется с экспериментальными данными. Наиболее вероятный тип связи фуллерен-лизин соответствует координации через группу £-nH2. Определены положения характеристических колебани2й, ответственных за связь фуллерен-лизин.
Acknowledgements
The research was supported by the Russian Science Foundation (RNF), project No. 23-2300064.
Благодарность
Исследование выполнено при поддержке Российского научного фонда (РНФ), проект № 23-2300064.
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Сведения об авторах
Rashad Abbas, Department of Pure Chemistry2Al-Baath University; graduate student, Department of Physical Chemistry St. Petersburg State Institute of Technology; Аббас Рашад, каф. химии Университета Аль-Баас; аспирант каф. физической химии СПбГТИ(ТУ)
Nikolay A. Charykov, Dr Sci. (Chem.), prof. of St. Petersburg State Institute of Technology; Чарыков Николай Александрович д-р хим. наук, проф. СПбГТИ(ТУ) [email protected]
Svetlana G. Izotova, Ph.D (Chem.), Head of the Department Physical Chemistry St. Petersburg State Institute of Technology Изотова Светлана Георгиевна, канд. хим. наук, зав. каф. физической химии СПбГТИ(ТУ), [email protected] Viktor A. Keskinov, Ph.D (Chem.), Associate Professor, Leading Researcher of Center of Excellence "VERITAS" D. Serikbaev East Kazakhstan State Technical University; Кескинов Виктор Анатольевич, канд. хим. наук, доц., вед. науч. сотр. Центра превосходства «VERITAS» ВКТУ им. Д. Серикбаева [email protected]
Dmitrii G. Letenko, Ph.D (Phys.-Math.), Associate Professor Saint Petersburg State University of Architecture and Civil Engineering (SPSUACE); Летенко Дмитрий Георгиевич, канд. физ.-мат. наук, доц. СПб архитектурно-строительного университета [email protected]
