Siyamak Shahab

Siyamak Shahab
International Sakharov Environmental Institute · Department of Ecological Chemistry and Biochemistry

Doctor of Sciences (Physical Chemistry) Professor of the Russian Academy of Natural History, PhD in Physical Chemistry

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279
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Introduction
Siyamak Shahab currently works at the Department of Biochemistry and Biophysics, International Sakharov Environmental University. Siyamak does research in Theoretical Chemistry, Medicinal Chemistry, Spectroscopy and Polymer Chemistry. His current projects are: 1) Theoretical investigation on the novel oxadiazole derivatives, 2) Development of Polarizer Films for the IR region of the Spectrum and 3) Antitumor and Antioxidant Properties of New Organic Compounds.

Publications

Publications (279)
Article
Graphical Abstract CO 2 Highlights  Physical adsorption of the CO and CO2 on Furanocoumarins  Investigation of the electronic properties after adsorption Co and CO2 on Furanocoumarins  Adsorption effect of the CO and CO2 on the natural charges of the Furanocoumarins  Comparison of the absorption spectra of the Furanocoumarins, before and after...
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In the present work, at first, density functional theory calculations were performed to investigate the molecular structure of the Chlorogenic, Ellagic, and Quisqualic acids by CAM�B3LYP/MidiX level of theory. A detail of quantum molecular descriptors of the title compounds such as ionization potential (IP) and Electron Affinities (EA), Hardness...
Article
We studied the adsorption of Resveratrol (RSV) drug on surfaces of the pure B12N12 and Mg‐decoration B12N12 fullerenes using density functional theory and time‐dependent density functional theory method at the B3PW91/6‐31+G* level of theory. The adsorption of RSV on two fullerenes is an exothermic process. The adsorption effect of the RSV molecule...
Article
In the current work, density functional theory calculations were carried out to evaluate the potential ability of apomorphine, dopamine, hinokitiol and deferiprone chelating agents to coordinate Mn²⁺, Fe³⁺ and Zn²⁺ metal ions with a 1:1 ratio in water solution. The binding energy values reveal that Zn²⁺/chelating agent complexes are more stable com...
Article
In the present work, the quantum chemical calculations of the molecular structures of the two newly synthesized dichroic dyes: 2-methoxy-4-((1E)-((4-(phenyldiazenyl)phenyl)imino)methyl)phenyl isonicotinate (IN-1); 2-methoxy-5-((1E)-((4-(phenyldiazenyl)phenyl)imino)methyl)phenyl isonicotinate (IN-2) have been predicted using Density Functional The...
Thesis
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Annotation. This article discusses the results of quantum chemical modeling of 3-(1-methylpyrrolidin-2-yl)pyridine (nicotine) and its agonist 6,10-methano-6H-pyrazino[2,3-h][3]benzazepine (varenicline) carried out using the chemical packages ChemOffice 2016, Gaussian 09W and GaussView 5.0 using the molecular mechanics method MM2 and the semi-empiri...
Conference Paper
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В этом исследовании разработана модель молекулы Sunitinib-2 на основе оригинальной молекулы Sunitinib. Изучены электрические свойства как оригинальной (1), так и модифицированной (2) молекулы Sunitinib. При расчетах был использован метод молекулярной механики MM2 программного пакета ChemBioOffice 2016 для квантово-химического моделирования.
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В данной работе изучены фармакокинетические свойства молекул Rosiglitazone и модифицированная Rosiglitazone-2. При исследовании использовались веб-сайты SwissADME, Biosig lab и pkCSM.
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Molecular docking and in silico analysis of novel epoxyisoindole derivatives as effective drug candidates for treatment of Parkinson’s disese were reported
Article
The charge transfer complex of drugs is an important means to study the binding mechanism of drugs and receptors. Here, the ground state structure and CT transition of the complex generated by the reaction of hydrogen peroxide (H 2 O 2) with the five antibiotics (TMP, NOR, OFL, CIP, and SMR) were theoretically investigated by density functional the...
Conference Paper
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The pharmacokinetic properties of rosemary, ferulic and syringic acids have been analyzed for the development of medicinal substances based on them. Their bioavailability was assessed using the SwissADME In-ternet resource. Their high bioavailability is shown.
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Описан молекулярный докинг между белком ID 6VPZ и перспективным лигандом С31H32N4O6 для лечения ВИЧ-1
Conference Paper
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Представлен молекулярный докинг между белком ID 7C62 и перспективным лигандом С20H19NO7 для лечения болезни Паркинсона
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Описана антимикробная активность и сенсорные свойства пиридиновых производных 4-аминоазобензола и куркумина
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Повышенное внимание международной общественности к ревматологии связано с тем, что аутоиммунные заболевания представляют собой хроническую патологию, требующую постоянного дорогостоящего лечения. Возрастание числа случаев заболеваний среди лиц трудоспособного возраста - приводит к росту временной и стойкой нетрудоспособности у половины пациенто...
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В настоящей работе проведено квантово-химическое моделирование 8-Хлор-1-метил-6-фенил4Н-[1,2,4]триазоло[4,3-а][1,4] бензодиазепина в газовой фазе и в состоянии сольватации водой с помощью неэмпирического метода RHF. Исследована электронная структура соединения. Рассчитаны электронные свойства, такие как ЕНОМО и ЕLUMO, а так же ширина запрещенной з...
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Проведено квантово-химическое моделирование 1H-индол-3-илгидрогенсульфата неэмпирическим методом CAM-B3-LYP/MidiX. Рассчитаны электронный спектр молекулы и ширина запрещенной зоны в вакууме.
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Синтезированы различные (E,E)-азоазометины конденсацией сложных эфиров никотиновой/изоникотиновой кислот с 4-аминоазобензолом в метаноле. Кватернизацией альдегидоэфиров и (E,Е)-азоазометинов в растворе дихлорметана в присутствии избытка йодметана получены соответствующие йодметилаты. Проведена оценка антимикробной активности соединений в отношении...
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В статье изучается применение молекулы C20H19NO7 в качестве лиганда, способного образовывать водородные связи с белком болезни Паркинсона ID 7C62. Успешное взаимодействие молекулы C20H19NO7 с белком ID 7C62 открывает перспективы для дальнейших исследований и разработки новых методов лечения болезни Паркинсона.
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В настоящей работе проведено квантово-химическое моделирование 4-(2-бромфенил)-6-(2,4-бромфенил)-N-(2-метил-5-нитрофенил)пиримидин-2-амина с использованием метода теории функционала плотности (DFT/B3LYP) с базисом MidiX. Исследована электронная структура соединения. Рассчитаны электронные свойства, такие как ЕНОМО и ЕLUMO, а также ширина запрещенн...
Conference Paper
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У працы прыведзены вынікі малекулярнага докінга паміж бялком 1 P5F і нарынгенінам. 1 p5f бялок, які задзейнічаны ў метабалічных шляхах хваробы Паркінсана (PARK 7). Мэта нашага даследавання - вывучыць магчымасць фарміравання тэрмадынамічна ўстойлівага комплексу паміж бялком 1P5F і нарынгенінам.
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Проведено квантово-химическое моделирование батрахотоксина полуэмпирическим методом PM6. Рассчитаны электронный спектр молекулы и ширина запрещенной зоны в среде вакуума.
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Проведено квантово-химическое моделирование природных биологически активных веществ: ресвератрола и куркумина. Рассчитана их антиоксидантная активность - ширина запрещённой зоны, энергии граничных орбиталей HOMO и LUMO. Изучены фармакокинетические свойства структур с помощью интернет ресурсов: Molinspiration и Swiss Dock. Установлено, что данные с...
Conference Paper
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В работе приведены полуэмпирические и теоретические расчеты молекулы 4-формил-2-метоксифенил (3as,6r,7s,7ar)-2-метил-1-оксо-1,2,3,6,7,7a-гексагидро-3a,6-эпоксиизоиндол-7-карбоксилата, в среде растворителя (вода), ее спектр поглощения и оптимизированная структура со значением полной энергии системы.
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В работе представлено новое производное морфолина: 2,4-ди-терт-бутил-6-морфолинофенол, которое может служить потенциальной лекарственной субстанцией против ВИЧ 1 типа. Проведена оценка его биологической активности с помощью программного пакета Gaussian09W методом B3LYP/Midix. При проведении молекулярного докинга выявлено образование термодинамическ...
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В работе приведены полуэмпирические и теоретические расчеты молекулы 5-формил-2-метоксифенил (3as,6r,7s,7ar)-2-метил-1-оксо-1,2,3,6,7,7a-гексагидро-3a,6-эпоксиизоиндол-7-карбоксилата, в среде растворителя (вода), ее спектр поглощения и оптимизированная структура со значением полной энергии системы.
Article
In this study, the interaction of Penicillamine anticancer drug with the B12P12, Ga12P12, and B6Ga6P12 nano-cages was studied using the DFT method. The negative values of Eads represent that the adsorption process is exothermic. The adsorption of PCA through the Osingle bondH over nano-cages has a lower EG rather other atoms of PAC. The highest ΔN...
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Acylation of substituted hydroxybenzaldehydes with hydrochloride of atophane acylchloride in dichloromethane in the presence of triethylamine gave esters, capable of forming (E)-azomethines when condensed with amines (4-aminoazobenzene, 4-aminoantipyrine) in methanol. In addition, an ester of atophane with a natural fragment of curcumin was obtaine...
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This review provides insight into the fate and removal of antibiotics in hospital wastewater, and demonstrates the occurrence and risk of antibiotics in hospital wastewater by different treatment processes and materials. The properties of typical antibiotics such as sulfonamides, tetracyclines and quinones in hospital wastewater were comprehensivel...
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A superior photoelectrochemical (PEC) aptasensor was manufactured for the detection of Escherichia coli (E. coli) based on a hybrid of triazine-based covalent–organic framework (COF) and cuprous oxide (Cu2O). The COF synthesized using 1,3,5-tris(4-aminophenyl)-benzene (TAPB) and 1,3,5-triformylphloroglucinol (Tp) as building blocks acted as a scaff...
Article
The adsorption of the dibenzothiophene (DBT) molecule upon the boron nitride nanosheet (BNNS) was discussed using the DFT method by M062X/6-311 + G* level of theory in the water solvent. The results of thermochemical parameters display the interaction of the DBT with BNNS is a spontaneous and exothermic process. The UV/Vis absorption analysis was c...
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Exposure to native starch by ionizing radiation is a promising and environmentally safe technology for purposefully changing the physico-chemical properties of starch. The environmental friendliness of irradiated starch due to the possibility of its use in various spheres of human life. It can be a good sorbent of heavy metals and radioactive isoto...
Article
In thе prеsеnt work, аt first, dеnsity functionаl thеory cаlculаtions wеrе pеrformеd to invеstigаtе thе molеculаr structurе of thе new piperazinе derivаtives by B3LYP/6-311+G* lеvеl of thеory. А dеtаil of quаntum molеculаr dеscriptors of thе titlе compounds such аs Ionizаtion Potеntiаl (IP) аnd Еlеctron Аffinitiеs (ЕА), Hаrdnеss (η), Softnеss (S),...
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In this report we briefly evaluate economic, ecological, scaling and computing issues for a hypothetical computing cluster built from old Android devices, that we propose for protein-protein docking test running cluster.
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Lysergol is a secondary metabolite of the ergoline family secreted by the parasitic fungi of genus Claviceps. Lysergol synergistically enhances the properties of some antibacterial drugs [1]. It was also found that lysergol can increase the bioavailability of some antibiotics [2]. This work presents the data of theoretical and semiempirical calcula...
Conference Paper
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A convenient method for the synthesis atophane esters with fragments of curcumin, azo-benzene, natural hydroxybenzaldehydes and their synthetic analogues, as well as a pyrazolone fragment was developed, and their antibacterial activity was studied.
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Molecular docking of insulin with potential inhibitors of aggregation was carried out in the study in order to predict the formation of possible complexes. Low molecular weight cAMP and Ap₄A compounds were optimized by DFT with the B3LYP/6-31G(d,p) functional, molecular dynamics calculations were performed for the resulting insulin protein complexe...
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This article presents the results of theoretical calculations of the compound (2R,3R)-3,3a-dihydroxy-6-imino2,3,3a,9a-tetrahadro-6H-four[2,3,4,5]oxazolo[3,2-a]pyrimidin-2-yl)methyl dihydrogen phosphate to determine its equilibrium geometry, free energy and the type of molecular orbitals involved in the formation of the absorption spectrum.
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This paper represents theoretical calculations related to newly synthetized oxopyrimidin compound 5-(4-amino2-oxopyrimidin-1(2h)-yl)-3,4- dihydroxytetrahydrofuran-2-yl)methyl dihydrogen phosphate in order to define its optimized geometry, free energy and form of molecular orbitals participated in formation of UV/Vis spectrum.
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In this paper, quantum chemical modeling of 3-(4-nitrophenyl)-5-(2,6-dimethylphenyl)-1H-pyrazole and 3-(2-bromophenyl)-5-(4-bromophenyl)-1H-pyrazole was carried out using the semi-empirical PM6 method. The electronic structure of the compound is investigated. Electronic properties, such as EНOMO and ELUMO, as well as the band gap width as the main...
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Pakinson’s disease is a global problem that requires new methods and approaches to both treatment and research. To date, the therapy of this disease is exclusively symptomatic. Our study demonstrates the possibility of using myricetin as a ligand that is able to form stable hydrogen bonds with the 3LFN protein of Parkinson’s disease.
Article
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In this study, we report the results of experiments and density functional theory (DFT), time-dependent DFT, and quantitative structure-activity relationship (QSAR) analyses of (2R,3S,4S,5R)-2-(2-amino-6-methoxy-9H-purin-9-yl)-5-(hydroxymethyl) tetrahydrofuran-3,4-diol (nelarabine). The molecular geometry, vibrational modes, excited states, molecul...
Article
In this work, four derivatives of arginine with biologically active acids: acetylsalicylic, butyric, nicotinic, and succinic acids were obtained and characterized using UV-visible, IR, 1 H NMR, and 13 C NMR spectroscopy. In addition to spectroscopic analyses, DFT calculations were applied to predict the physico-chemical properties of the studied co...
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Predicting adsorption behavior of the Triacanthine (TRC) anticancer drug on the surface of B12N12 nano-cage was investigated using DFT and TD-DFT methods by B3LYP/6-311+G(d) level in the water solution. The adsorption energies of the TRC-B12N12 complexes (A-C) were shown that the adsorption process is exothermic. The UV/Vis absorption and IR spectr...
Article
In the present work, at first, DFT calculations were carried out to study the molecular structure of the tenofovir at B3LYP/MidiX level of theory and in the water as solvent. The HOMO/LUMO molecular orbitals, excitation energies and oscillator strengths of investigated drug were also calculated and presented. NBO analysis was performed to illustrat...
Article
In the present work, at first, DFT calculations were carried out to study the molecular structure of the tenofovir at B3LYP/MidiX level of theory and in the water as solvent. The HOMO/LUMO molecular orbitals, excitation energies and oscillator strengths of investigated drug were also calculated and presented. NBO analysis was performed to illustrat...
Article
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In the present work, at first, density functional theory (DFT) calculations were utilized for the molecular design of the four new butanoic acid derivatives at the B3LYP/6-31+G(d) level of theory. After DFT calculations, synthesis, FT-IR, 1H NMR, and 13C NMR spectra of corresponding molecules were presented. The NBO analysis and electronic properti...
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Пленки на основе поливинилового спирта (ПВС) находят применение в качестве биодеградируемых упаковочных материалов. Эти пленочные материалы обладают высокими барьерными свойствами и могут использоваться в пищевой отрасли, медицине, химической промышленности. С целью улучшения функциональных характеристик и расширения областей применения разрабатыва...
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This publication presents theoretical calculations applied to N-(3,5-di-tert-butyl-2-hydroxyphenyl) methanesulfonamide compounds to determine their optimized state, predict its free energy, and determine the molecular orbitals involved in spectrum formation.
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Квантово-химическое моделирование взаимодействия между молекулами гуанозина в водном растворе показало возможность существования димера, стабилизированного водородными связями с участием аминогруппы и карбонильного атома кислорода гетерооснования одной молекулы и атома кислорода 3′-ОН группы и атома водорода 2′-ОН группы другой молекулы, соответст...
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This paper presents theoretical calculations applied to N-(2-hydroxy-3,5 diisopropylphenyl)methanesulfonamide to determine its optimal free energy state and the shape of the molecular orbitals involved in the formation of the UV/Vis spectrum.
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This paper represents theoretical calculations applied to newly synthesized of N-(3,5-di-tert-butyl-2-hydroxyphenyl)-4-methylbenzenesulfonamide compounds for defining their optimized state, predicting its free energy, and distinguishing molecular orbitals participating in spectrum formation
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This paper represents theoretical calculations related to newly synthesized methanesulfonamide compounds for defining their optimized state, predicting its free energy, and distinguishing molecular orbitals participating in spectrum formation.
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The paper presents the data of semi-empirical and theoretical calculations of molecules in the medium of the solvent, their absorption spectrum and the optimized structure with the value of the total energy of the system.
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This paper presents theoretical calculations related to N-(3,5-di-tert-butyl-2-hydroxyphenyl) benzene sulfonamide compound to determine its equilibrium geometry, total energy and calculation of molecular orbitals involved in formation of UV/Vis spectrum.
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The paper presents the data of semi-empirical and theoretical calculations of molecules in the medium of the solvent, their absorption spectrum and the optimized structure with the value of the total energy of the system.
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This publication presents theoretical calculations applied to 2,4-di-tert-butyl-6-morpholinophenol compounds to determine their optimized state, predict its free energy and determine the molecular orbitals involved in spectrum formation.
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This paper represents theoretical calculations applied to newly synthesized 2,4-di-tert-butyl-6-(p-tolylamino) phenol compounds for defining their optimized state predicting its free energy and distinguishing molecular orbitals participating in spectrum formation.
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The paper presents the data of semi-empirical and theoretical calculations of molecules in the medium of the solvent, their absorption spectrum and the optimized structure with the value of the total energy of the system.
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This paper represents theoretical calculations related to newly synthesized phenol compound for defining its optimized geometry, free energy and form of molecular orbitals participated in formation of UV/Vis spectrum.
Article
In the present research, the interaction of chlormethine (CM) anticancer drug through its two sites (N and Cl) with the X3O-B12N12 nano-cages (X = Li, Na, K) was investigated using the DFT method at the B3LYP/6-31g(d,p) level of theory in the gas phase and water solution. The adsorption effects on the bond lengths, electronic properties, dipole mom...
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Рассмотрены теоретические сведения, включающие информацию о молекуле аденозинмонофосфата (АМФ). Изучены его физико-химические свойства. Проведено квантово-химическое моделирование молекулы АМФ, а также рассчитан спектр поглощения молекулы полуэмпирическим методом PM6.
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В настоящее время активно изучаются свойства проводящих полимеров (полупроводников) полианилина (ПАНИ), который проявляет окислительно-восстановительную активность, отличается высокой термической стабильностью и химической активностью и полипиррола (Ппир), обладающего высокой электрической проводимостью в допированном состоянии, зависящей от кисл...
Article
In this research, a DFT calculation was performed for study to investigate the encapsulation of the anticancer drug Ibrance into CNT(8,8-7) by using M062X/6-311G * level of theory in the solvent water. TD-DFT method was used to compute the electronic spectra of the Ibrance drug, CNT(8,8-7) and complex CNT(8,8-7)/Ibrance in aqueous medium for the st...
Article
The adsorption of the Zejula drug on the surface of B12N12 nanocluster has studied using DFT and TD-DFT. The quantum calculations have performed at the M062X/6–311 + + G(d,p) level of theory in the solvent water. The adsorption of the Zejula from N13 atom on the B12N12 leads to the higher electrical conductivity due to the low Eg rather. The change...
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Разработан удобный одностадийный метод синтеза новых производных бисакридина, содержащих фраг-менты 5-арилизоксазолов, 4,5-дихлоризотиазола, а также остатки изоникотиновой кислоты, ковалентно присоединенных с помощью сложноэфирных групп в различные положения ароматического ядра. Трех-компонентную каскадную конденсацию 1,5-нафталиндиамина, различных...
Article
Разработан удобный одностадийный метод синтеза новых производных бисакридина, содержащих фрагменты 5-арилизоксазолов, 4,5-дихлоризотиазола, а также остатки изоникотиновой кислоты, ковалентноприсоединенных с помощью сложноэфирных групп в различные положения ароматического ядра. Трехкомпонентную каскадную конденсацию 1,5-нафталиндиамина, различных ал...
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In the study, for the first time, the physicochemical properties of (Z)-4-(2-hydroxybenzylidene)-3-methylisoxazole-5(4H)-one were calculated using the theory of density functions. The energies HOMO, LUMO, bandgap (Eg), ionization potential (IP), electron affinity (EA), hardness (η), softness (S) and electronegativity (μ) were calculated.
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The problem of ambient air pollution is one of the priority problems of modern science, and the search for innovative ways to clean it is one of its main directions. The use of computational chemistry methods to study the physicochemical, adsorption properties of molecules, in comparison with experimental studies, significantly accelerates the obta...
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The paper presents the results of physical sorption of 6-thio-2'-deoxyguanosine (6-thio-dG) and 6-methyl-2-ethyl-pyridine-3-ol with a CNT nanotube (10, 10-8).
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The theoretical information concerning the adenosine monophosphate molecule is considered, and its biological characteristics are determined.
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A simple method for the preparation of AMPPD, the precursor of the biological fluorescent probe, is reported. Using cheap and easily available methyl m-hydroxybenzoate and adamantane as raw materials, the condensation product was obtained by McMurry reaction and then reacted with phosphorus oxychloride to realize the phosphorylation process, and th...
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With the help of the Internet resource Molinspiration, the calculation of the main biological parameters of fludarabine has been performed. The fludarabine molecule was evaluated according to Lipinski's rule. It was found that drugs synthesized on the basis of fludarabine have high biological activity.
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