A systematic benchmark of the ab initio Bethe-Salpeter equation approach for low-lying optical excitations of small organic molecules

The predictive power of the ab initio Bethe-Salpeter equation (BSE) approach, rigorously based on many-body Green's function theory but incorporating information from density functional theory, has already been demonstrated for the optical gaps and spectra of solid-state systems. Interest in photoactive hybrid organic/inorganic systems has recently increased, and so has the use of the BSE for computing neutral excitations of organic molecules. However, no systematic benchmarks of the BSE for neutral electronic excitations of organic molecules exist. Here, we study the performance of the BSE for the 28 small molecules in Thiel's widely-used time-dependent density functional theory benchmark set [M. Schreiber et al. J. Chem. Phys. 128, 134110 (2008)]. We observe that the BSE produces results that depend critically on the mean-field starting point employed in the perturbative approach. We find that this starting point dependence is mainly introduced through the quasiparticle energies obtained at the intermediate GW step, and that with a judicious choice of starting mean-field, singlet excitation energies obtained from BSE are in excellent quantitative agreement with higher-level wavefunction methods. The quality of the triplet excitations is slightly less satisfactory

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Комплекс цефтриаксона с Mg(II): синтез, структура, спектральные и антибактериальные свойства

Magnesium complex of ceftriaxone was obtained and characterized by atomic-emission and elemental analysis, TGA, FTIR and Raman spectroscopy, X‑ray diffraction and density functional theory calculations. Ceftriaxone was coordinated to the magnesium ion by the oxygen of the triazine cycle in the 6th position, the nitrogen of the amine group of the thiazole ring, and oxygen atoms of the lactam carbonyl and carboxylate groups. The disodium salt of ceftriaxone and magnesium complex were screened for antibacterial activity against Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosaПолучен и охарактеризован магниевый комплекс цефтриаксона методами атомно-эмиссионного и элементного анализов, ТГА, ИК- и КР‑спектроскопии, РФА и расчетов теории функционала плотности. Цефтриаксон координируется к иону магния через кислород триазинового цикла в шестом положении, азот аминогруппы тиазольного цикла и атомы кислорода карбоксильной и лактамной групп. Динатриевая соль цефтриаксона и комплекс магния были исследованы на антибактериальную активность в отношении Staphylococcus aureus, Escherichia coli и Pseudomonas aeruginos

Потенциальные противомикробные агенты на основе тимидина с помощью расчетов In Silico DFT

Modification of the hydroxyl (–OH) group of thymidine by acylation may cause changes in the antimicrobial and anticancer properties of thymidine which is investigated in this study. The current study is concentrated towards the in silico computational study of different in silico and bioactivity investigations. We relate the optimization of thymidine and its acylated analogs by applying density functional theory (DFT) with B 3LYP/3–21G level theory to demonstrate their thermal, frontier molecular orbital, the density of states (DOS) and molecular electrostatic potential (MESP) properties. All the analogs were found with enriched score than their parent atom which indicates the theoretical stability of these compounds. To deeply realize these observations molecular docking studies have been performed against human PARP1 (E.coli-BL21, PDB: 4ZZZ) and remarkable binding energies and non-covalent interactions were observed. Bioactivity data exhibited that compounds consisted of standard values in predicted cases. Moreover, toxicity data showed a safer level of the score for all studied thymidine analogs. This work demonstrates that potential thymidine analogs bind to bacterial pathogens for circumventing their activities and opens avenues for the development of newer drug candidates that can target bacterial and fungal pathogensМодификация гидроксильной (–OH) группы тимидина путем ацилирования может вызвать изменения в антимикробных и противоопухолевых свойствах тимидина, которые исследуются в данной работе. Текущее исследование сосредоточено на вычислительном изучении in silico различных исследований in silico и биоактивности. Мы связываем оптимизацию тимидина и его ацилированных аналогов с применением теории функционала плотности (DFT) с теорией уровней B 3LYP/3–21G, чтобы продемонстрировать их тепловые свойства, пограничную молекулярную орбиталь, плотность состояний (DOS) и молекулярный электростатический потенциал (MESP). Все аналоги были обнаружены с показателем, превышающим их исходный атом, что указывает на теоретическую стабильность этих соединений. Чтобы глубже осознать эти наблюдения, были проведены исследования молекулярного докинга против PARP1 человека (E.coli-BL21, PDB: 4ZZZ) и обнаружены значительные энергии связи и нековалентные взаимодействия. Данные о биологической активности показали, что соединения в прогнозируемых случаях соответствовали стандартным значениям. Более того, данные о токсичности показали более безопасный уровень оценки для всех изученных аналогов тимидина. Эта работа демонстрирует, что потенциальные аналоги тимидина связываются с бактериальными патогенами, чтобы обойти их активность, и открывает возможности для разработки новых лекарственных препаратов-кандидатов, которые могут воздействовать на бактериальные и грибковые патоген

Synthesis, spectroscopic characterizations and DFT studies on the metal complexes of azathioprine immunosuppressive drug

ABSTRACT. A complex of the immunosuppressive drug azathioprine with Cr(II), Mn(II), Fe(II), Zn(II), Cu(II), Ni(II), and Co(II) were synthesized and characterized through spectroscopic and thermal studies. The infrared spectra show the coordination of azathioprine via N(9) to the metal, also, the range around 640–650 cm−1 remains unchanged in the complexes, indicating the possibility that the ether group may not be involved in the binding. Thermogravimetric analysis (TG), thermogravimetric derivational analysis (DTG), and differential thermogravimetric analysis (DTA) have been studied in the temperature range from 0 °C to 1000 °C. The study of pyrolysis showed that all complexes decompose in more than one step and that the final decomposition product is metal oxide. The DFT (density functional theory) with B3LYP/6-31G++ level of theory was used to study the optimized geometry, HOMO→LUMO energy gap, and molecular electrostatic potential map of azathioprine before and after deprotonation.                 KEY WORDS: Azathioprine, Spectral study, Thermal study, Decomposition products, DFT Bull. Chem. Soc. Ethiop. 2022, 36(1), 73-84.                                                                   DOI: https://dx.doi.org/10.4314/bcse.v36i1.

Estudio computacional conformacional, espectroscópico, ONL, HOMO–LUMO y reactividad de 1,3,5-trifenilpirazol

Os parâmetros estruturais do 1,3,5-trifenilpirazole foram determinados com DFT/cam-B3LYP com o conjunto de bases 6-311++G(d,p). Os resultados da estrutura molecular otimizada são apresentados e comparados com os dados de raios-X disponíveis da molécula ou moléculas muito semelhantes. Uma análise completa dos espectros observados das medições espectrais de FT-IR, RMN (1H e 13C) e absorção UV-Vis com TD-DFT na mesma função e conjunto de bases é fornecida. As propriedades NLO desta molécula também foram investigadas. As distribuições de cargas NPA e MEP estão correlacionadas. Os resultados calculados e os resultados experimentais são discutidos e correlacionados.The structural parameters of 1,3,5-triphenylpyrazole were determined with DFT/cam-B3LYP with the base set 6-311++G(d,p). The results of the optimized molecular structure are presented and compared with the available X-ray data of the molecule or very similar molecules. A complete analysis of the observed spectra of the spectral measurements of FT-IR, NMR (1H and 13C) and UV-Vis absorption with TD-DFT in the same function and set of bases is provided. The descriptors of global and local reactivity have been determined. The NLO properties of this molecule were also investigated. The distributions of NPA and MEP loads are correlated. The calculated results and the experimental findings are discussed and correlated.Los parámetros estructurales de 1,3,5-trifenilpirazol se determinaron con DFT/cam-B3LYP con el conjunto de bases 6-311++G(d,p). Los resultados de la estructura molecular optimizada se presentan y comparan con los datos disponibles de rayos X de la molécula o moléculas muy similares. Se proporciona un análisis completo de los espectros observados de las mediciones espectrales de FT-IR, RMN (1H y 13C) y absorción UV-Vis con TD-DFT en la misma función y conjunto de bases. Los descriptores de reactividad global y local han sido determinados. Las propiedades NLO de esta molécula también fueron investigadas. Las distribuciones de cargas del análisis de poblaciones naturales y el mapa de potencial electrostáticos están correlacionadas. Los resultados calculados y los hallazgos experimentales se discuten y se correlacionan

Исследования по прогнозированию проходимости, ADMET и молекулярному докингу некоторых производных маннопиранозида против полимеразы NS 5B HCV

Several carbohydrate-based medications are now being used to treat a variety of human ailments all around the world. Therefore, we concentrated on computational investigations of previously synthesized methyl α-D‑mannopyranoside (MDM) derivatives. To determine the structural and thermodynamical properties of the modified derivatives, a quantum chemical research was conducted using Gaussian09 employing density functional theory (DFT). Molecular electrostatic potential (MEP) calculation has performed to calculate their possible electrophilic and nucleophilic attack. The binding energy and binding strategies of certain viral proteins from the Hepatitis C virus (2IJN, 3MWV, and 3FKQ) were investigated using molecular docking simulations, and adequate binding affinity was discovered. ADMET calculations predict the improved pharmacokinetic properties with better drug-likeness profile of all MDM derivatives. Finally, these compounds can be described as molecules with high antiviral/antimicrobial potential that have been modified in terms of their structural side chains in α-D‑mannopyranoside sequenceНесколько препаратов на основе углеводов в настоящее время используются для лечения различных заболеваний человека по всему миру. Поэтому мы сосредоточились на вычислительных исследованиях ранее синтезированных производных метил-α-D‑маннопиранозида (MDM). Чтобы определить структурные и термодинамические свойства модифицированных производных, было проведено квантово-химическое исследование с применением Gaussian 09 и с использованием теории функционала плотности (DFT). Был проведен расчет молекулярного электростатического потенциала (MEP) для расчета их возможной электрофильной и нуклеофильной атаки. Энергия связывания и стратегии связывания определенных вирусных белков вируса гепатита С (2IJN, 3MWV и 3FKQ) были исследованы с использованием моделирования молекулярного докинга, и была обнаружена адекватная аффинность связывания. Расчеты ADMET предсказывают улучшенные фармакокинетические свойства с лучшим профилем лекарственного подобия всех производных MDM. Наконец, эти соединения могут быть описаны как молекулы с высоким противовирусным/антимикробным потенциалом, которые были модифицированы с точки зрения их структурных боковых цепей в последовательности α-D‑маннопиранозид

Organic Peroxides in Radical Chemistry and Stereochemical Study of the Intramolecular Schmidt Reaction

Organic peroxides and organic azides are highly energetic functional groups and have been utilized in many synthetic applications for over a hundred years. The first part of this thesis focuses on organic peroxides as a source of radicals. After a general introduction to organic peroxides in radical chemistry in chapter 1, peroxyoxalates and diacyl peroxides move into the focus of this thesis (chapters 2-5). Di-tert-butyl peroxyoxalates (DTBPO) was found to be an ideal radical initiator in the key step of our short enantioselective synthesis of the natural product (+)-brefeldin C described in chapter 2. Inspired by the thermal decomposition of DTBPO, peroxyoxalates were studied as a source of tertiary alkoxy radicals. An operationally simple method to access these radicals from tertiary alkyl hydroperoxides was developed using oxalyl chloride and is presented in chapter 3. The alkoxy radicals have been used in particular for the synthesis of various 4’ functionalized alcohols via 1,5-hydrogen atom transfer and subsequent trapping of the relocated radical with a suitable radical trap. The one-pot procedure is fast, does not require workup after the reaction, and yields the functionalized alcohols in moderate to excellent yields. Unpublished results from work using this method and investigations on an analogous mechanism based on borinate radicals are compiled in chapter 4. Due to the unstable nature of organic peroxides and the hazards associated with their handling, a safer approach to their synthesis and direct use in continuous flow was investigated in chapter 5. It has been found that clean dilauroyl peroxide can be formed in excellent yield and can be used directly as an initiator in a subsequent reaction that is connected in series. In the second part of this thesis, the stereochemical challenges of the intramolecular Schmidt reaction and the strategies to address them are introduced in chapter 6. Our investigations to control the stereochemistry of the triflate-mediated intramolecular Schmidt reaction are summarized in two draft manuscripts in chapters 7 and 8. Our group has developed a protocol to run the reaction under nonacidic conditions using azidotriflates: After an initial intramolecular SN2 reaction between the azide and the triflate moiety, an intermediate aminodiazonoium salt is formed, which undergoes a stereoselective 1,2-shift with concomitant N2 elimination. The substitution has been found to proceed highly stereospecifically. The formed iminium triflate is reduced diastereoslectively in a second step to the bicyclic amine. Remarkably, the chiral alcohol center controls the entire process and thus only one of the four possible diastereomers is obtained in a highly selective manner. The method has been used for the concise synthesis of a lehmizidine- and an indolizidine alkaloid that represent components of myrmicaria melanogaster ant venom. It was further investigated whether the method is applicable to access bridgehead-functionalized azabicycles from the corresponding prefunctionalized azidoalcohols. The results of this study complement previous finding that have been conducted in two precedent PhD theses and are presented in the last chapter of this thesis